I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 28 05:32:58 +14 2024 I: pbuilder-time-stamp: 1706369578 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gromacs_2022.5-2.dsc] I: copying [./gromacs_2022.5.orig-regressiontests.tar.gz] I: copying [./gromacs_2022.5.orig.tar.gz] I: copying [./gromacs_2022.5-2.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Feb 16 06:03:34 2023 gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F gpgv: issuer "nbreen@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gromacs_2022.5-2.dsc: no acceptable signature found dpkg-source: info: extracting gromacs in gromacs-2022.5 dpkg-source: info: unpacking gromacs_2022.5.orig.tar.gz dpkg-source: info: unpacking gromacs_2022.5.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2022.5-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch dpkg-source: info: applying manual-image-conversion.patch dpkg-source: info: applying disable-gmxtimingtests.patch dpkg-source: info: applying python3-collections-iterable.patch dpkg-source: info: applying muparser-older-version.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2889789/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 27 15:33 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2889789/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2889789/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=00b88395b1a64802b2f8a0698e3748d0 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2889789 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.a64QXxT7/pbuilderrc_4aTO --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.a64QXxT7/b2 --logfile b2/build.log gromacs_2022.5-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 23 2023 more -rwsr-xr-x 1 root root 59704 Mar 23 2023 mount -rwxr-xr-x 1 root root 18744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 9 Jan 27 15:33 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 23 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/2889789/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.3), libx11-dev, lsb-release, mpi-default-bin, mpi-default-dev, pkg-config, zlib1g-dev, doxygen, ghostscript, graphicsmagick, graphviz, mscgen, python3-sphinx, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18148 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on cmake (>= 3.13); however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libhwloc-dev; however: Package libhwloc-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libmuparser-dev (>= 2.3.3); however: Package libmuparser-dev is not installed. pbuilder-satisfydepends-dummy depends on libx11-dev; however: Package libx11-dev is not installed. pbuilder-satisfydepends-dummy depends on lsb-release; however: Package lsb-release is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-bin; however: Package mpi-default-bin is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on graphicsmagick; however: Package graphicsmagick is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on mscgen; however: Package mscgen is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind is not installed. pbuilder-satisfydepends-dummy depends on symlinks; however: Package symlinks is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} ca-certificates{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-lmodern{a} fonts-urw-base35{a} gettext{a} gettext-base{a} gfortran-12{a} ghostscript{a} graphicsmagick{a} graphviz{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libabsl20220623{a} libann0{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif15{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcbor0.8{a} libcdt5{a} libcgraph6{a} libclang-cpp14{a} libclang1-14{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2{a} libcurl4{a} libdatrie1{a} libdav1d6{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran-12-dev{a} libgfortran5{a} libglib2.0-0{a} libgraphicsmagick-q16-3{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libhwy1{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu72{a} libidn12{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp25{a} libjxl0.7{a} libkpathsea6{a} liblab-gamut1{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm14{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmunge2{a} libmuparser-dev{a} libmuparser2v5{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenjp2-7{a} libopenmpi-dev{a} libopenmpi3{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpciaccess0{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpmix-dev{a} libpmix2{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} libptexenc1{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librav1e0{a} librdmacm1{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsm6{a} libssh2-1{a} libsub-override-perl{a} libsvtav1enc1{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libtexluajit2{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{a} libuv1{a} libwebp7{a} libwebpmux3{a} libwmflite-0.2-7{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx265-199{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxnvctrl0{a} libxpm4{a} libxrender1{a} libxt6{a} libyuv0{a} libz3-4{a} libzzip-0-13{a} lsb-release{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} mscgen{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-tz{a} python3-urllib3{a} python3.11{a} python3.11-minimal{a} rdfind{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} symlinks{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} x11-common{a} x11proto-dev{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus default-jre dvisvgm fonts-droid-fallback fonts-liberation2 fonts-texgyre fonts-texgyre-math javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libfile-mimeinfo-perl libglib2.0-data libgts-bin libjson-xs-perl libldap-common libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libspreadsheet-parseexcel-perl libx11-protocol-perl lmodern lynx psmisc publicsuffix python3-pil ruby shared-mime-info texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xauth xdg-user-dirs 0 packages upgraded, 290 newly installed, 0 to remove and 0 not upgraded. Need to get 292 MB of archives. After unpacking 1251 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 12 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2023c-5+deb12u1 [296 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 bash-completion all 1:2.11-6 [234 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2+deb12u1 [989 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u4 [390 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 docutils-common all 0.19+dfsg-6 [127 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libllvm14 amd64 1:14.0.6-12 [21.8 MB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libclang-cpp14 amd64 1:14.0.6-12 [11.1 MB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libclang1-14 amd64 1:14.0.6-12 [6157 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 doxygen amd64 1.9.4-4 [4611 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libgfortran-12-dev amd64 12.2.0-14 [834 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 gfortran-12 amd64 12.2.0-14 [10.2 MB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libgs-common all 10.0.0~dfsg-11+deb12u2 [148 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libgs10-common all 10.0.0~dfsg-11+deb12u2 [586 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.10-1~deb12u1 [201 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3+deb12u5 [245 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libidn12 amd64 1.41-1 [83.8 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libijs-0.35 amd64 0.35-15 [16.4 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libjbig2dec0 amd64 0.19-3 [67.2 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2 [189 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libgs10 amd64 10.0.0~dfsg-11+deb12u2 [2465 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 ghostscript amd64 10.0.0~dfsg-11+deb12u2 [56.8 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libaom3 amd64 3.6.0-1 [1851 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libdav1d6 amd64 1.0.0-2 [495 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libde265-0 amd64 1.0.11-1+deb12u1 [185 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libx265-199 amd64 3.5-2+b1 [1150 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libheif1 amd64 1.15.1-1 [215 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libhwy1 amd64 1.0.3-3+deb12u1 [348 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libjxl0.7 amd64 0.7.0-10 [1046 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2+deb12u1 [109 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libwmflite-0.2-7 amd64 0.2.12-5.1 [75.2 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libgraphicsmagick-q16-3 amd64 1.4+really1.3.40-4 [1180 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 graphicsmagick amd64 1.4+really1.3.40-4 [1019 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libann0 amd64 1.1.2+doc-9+b1 [25.1 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libcdt5 amd64 2.42.2-7+b3 [39.8 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libcgraph6 amd64 2.42.2-7+b3 [63.2 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libabsl20220623 amd64 20220623.1-1 [391 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libgav1-1 amd64 0.18.0-1+b1 [332 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 librav1e0 amd64 0.5.1-6 [763 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libsvtav1enc1 amd64 1.4.1+dfsg-1 [2121 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libyuv0 amd64 0.0~git20230123.b2528b0-1 [168 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libavif15 amd64 0.11.1-1 [93.8 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libxpm4 amd64 1:3.5.12-1.1+deb12u1 [48.6 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libgd3 amd64 2.3.3-9 [124 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-5+b1 [160 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libltdl7 amd64 2.4.7-5 [393 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libpathplan4 amd64 2.42.2-7+b3 [42.2 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libgvc6 amd64 2.42.2-7+b3 [678 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libgvpr2 amd64 2.42.2-7+b3 [189 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 liblab-gamut1 amd64 2.42.2-7+b3 [198 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 libxmu6 amd64 2:1.1.3-3 [60.1 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 libxaw7 amd64 2:1.0.14-1 [201 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 graphviz amd64 2.42.2-7+b3 [611 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 libblas-dev amd64 3.11.0-2 [158 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 libevent-2.1-7 amd64 2.1.12-stable-8 [180 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-8 [107 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-8 [60.6 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 libevent-dev amd64 2.1.12-stable-8 [305 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 libfftw3-double3 amd64 3.3.10-1 [776 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 libfftw3-long3 amd64 3.3.10-1 [337 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libfftw3-quad3 amd64 3.3.10-1 [603 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libfftw3-single3 amd64 3.3.10-1 [806 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libfftw3-bin amd64 3.3.10-1 [51.7 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 libfftw3-dev amd64 3.3.10-1 [2123 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 libnuma-dev amd64 2.0.16-1 [35.0 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 libltdl-dev amd64 2.4.7-5 [164 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 libhwloc-dev amd64 2.9.0-1 [241 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-3~deb12u1 [13.5 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get: 206 http://deb.debian.org/debian bookworm/main amd64 libnl-3-dev amd64 3.7.0-0.2+b1 [104 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-dev amd64 3.7.0-0.2+b1 [203 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 libibverbs-dev amd64 44.0-2 [633 kB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 210 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 libkpathsea6 amd64 2022.20220321.62855-5.1+deb12u1 [152 kB] Get: 215 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 216 http://deb.debian.org/debian bookworm/main amd64 liblapack-dev amd64 3.11.0-2 [4631 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 libmuparser2v5 amd64 2.3.3-0.1 [144 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 libmuparser-dev amd64 2.3.3-0.1 [34.4 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+deb12u1 [622 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get: 222 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 libpmix-dev amd64 4.2.2-1+deb12u1 [902 kB] Get: 226 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get: 227 http://deb.debian.org/debian bookworm/main amd64 libopenmpi-dev amd64 4.1.4-3+b1 [970 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get: 229 http://deb.debian.org/debian bookworm/main amd64 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 libptexenc1 amd64 2022.20220321.62855-5.1+deb12u1 [43.7 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 233 http://deb.debian.org/debian bookworm/main amd64 libsynctex2 amd64 2022.20220321.62855-5.1+deb12u1 [59.8 kB] Get: 234 http://deb.debian.org/debian bookworm/main amd64 libteckit0 amd64 2.5.11+ds1-1+b1 [335 kB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 libtexlua53-5 amd64 2022.20220321.62855-5.1+deb12u1 [111 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 libtexluajit2 amd64 2022.20220321.62855-5.1+deb12u1 [246 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 x11proto-dev all 2022.1-1 [599 kB] Get: 239 http://deb.debian.org/debian bookworm/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 242 http://deb.debian.org/debian bookworm/main amd64 libxcb1-dev amd64 1.15-1 [181 kB] Get: 243 http://deb.debian.org/debian bookworm/main amd64 libx11-dev amd64 2:1.8.4-2+deb12u2 [837 kB] Get: 244 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get: 245 http://deb.debian.org/debian bookworm/main amd64 libzzip-0-13 amd64 0.13.72+dfsg.1-1.1 [58.3 kB] Get: 246 http://deb.debian.org/debian bookworm/main amd64 lsb-release all 12.0-1 [6416 B] Get: 247 http://deb.debian.org/debian bookworm/main amd64 mpi-default-bin amd64 1.14 [4752 B] Get: 248 http://deb.debian.org/debian bookworm/main amd64 mpi-default-dev amd64 1.14 [5548 B] Get: 249 http://deb.debian.org/debian bookworm/main amd64 mscgen amd64 0.20-14 [49.5 kB] Get: 250 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 251 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 252 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 253 http://deb.debian.org/debian bookworm/main amd64 tex-common all 6.18 [32.5 kB] Get: 254 http://deb.debian.org/debian bookworm/main amd64 preview-latex-style all 12.2-1 [201 kB] Get: 255 http://deb.debian.org/debian bookworm/main amd64 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 256 http://deb.debian.org/debian bookworm/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 257 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 258 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get: 259 http://deb.debian.org/debian bookworm/main amd64 python3-babel all 2.10.3-1 [103 kB] Get: 260 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get: 261 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 262 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 263 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 264 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 265 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B] Get: 266 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 267 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1 [39.4 kB] Get: 268 http://deb.debian.org/debian bookworm/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 269 http://deb.debian.org/debian bookworm/main amd64 python3-markupsafe amd64 2.1.2-1+b1 [13.2 kB] Get: 270 http://deb.debian.org/debian bookworm/main amd64 python3-jinja2 all 3.1.2-1 [119 kB] Get: 271 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 272 http://deb.debian.org/debian bookworm/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 273 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 274 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get: 275 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 276 http://deb.debian.org/debian bookworm/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 277 http://deb.debian.org/debian bookworm/main amd64 sphinx-common all 5.3.0-4 [653 kB] Get: 278 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB] Get: 279 http://deb.debian.org/debian bookworm/main amd64 rdfind amd64 1.5.0-1.1+b1 [41.3 kB] Get: 280 http://deb.debian.org/debian bookworm/main amd64 symlinks amd64 1.4-4 [11.3 kB] Get: 281 http://deb.debian.org/debian bookworm/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 282 http://deb.debian.org/debian bookworm/main amd64 tex-gyre all 20180621-6 [6209 kB] Get: 283 http://deb.debian.org/debian bookworm/main amd64 texlive-binaries amd64 2022.20220321.62855-5.1+deb12u1 [10.5 MB] Get: 284 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 285 http://deb.debian.org/debian bookworm/main amd64 texlive-base all 2022.20230122-3 [21.9 MB] Get: 286 http://deb.debian.org/debian bookworm/main amd64 texlive-fonts-recommended all 2022.20230122-3 [4988 kB] Get: 287 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-base all 2022.20230122-3 [1182 kB] Get: 288 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-recommended all 2022.20230122-3 [8880 kB] Get: 289 http://deb.debian.org/debian bookworm/main amd64 texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 290 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-extra all 2022.20230122-4 [19.2 MB] Fetched 292 MB in 13s (21.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package poppler-data. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18148 files and directories currently installed.) Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18998 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19432 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package tzdata. Preparing to unpack .../002-tzdata_2023c-5+deb12u1_all.deb ... Unpacking tzdata (2023c-5+deb12u1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../003-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package bash-completion. Preparing to unpack .../006-bash-completion_1%3a2.11-6_all.deb ... Unpacking bash-completion (1:2.11-6) ... Selecting previously unselected package openssl. Preparing to unpack .../007-openssl_3.0.11-1~deb12u2_amd64.deb ... Unpacking openssl (3.0.11-1~deb12u2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../008-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../009-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../010-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../011-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../012-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../013-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../014-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../015-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../016-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../017-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../018-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../019-libedit2_3.1-20221030-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:amd64. Preparing to unpack .../020-libcbor0.8_0.8.0-2+b1_amd64.deb ... Unpacking libcbor0.8:amd64 (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../021-libfido2-1_1.12.0-2+b1_amd64.deb ... Unpacking libfido2-1:amd64 (1.12.0-2+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../022-openssh-client_1%3a9.2p1-2+deb12u1_amd64.deb ... Unpacking openssh-client (1:9.2p1-2+deb12u1) ... Selecting previously unselected package ucf. Preparing to unpack .../023-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../024-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../025-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../026-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../027-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../028-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package chrpath. Preparing to unpack .../029-chrpath_0.16-2+b1_amd64.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../030-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../031-libxml2_2.9.14+dfsg-1.3~deb12u1_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../032-libarchive13_3.6.2-1_amd64.deb ... Unpacking libarchive13:amd64 (3.6.2-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../033-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../034-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../035-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../036-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../037-libnghttp2-14_1.52.0-1+deb12u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../038-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. 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Current default time zone: 'Etc/UTC' Local time is now: Sat Jan 27 15:36:06 UTC 2024. Universal Time is now: Sat Jan 27 15:36:06 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgts-0.7-5:amd64 (0.7.6+darcs121130-5+b1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up libfontenc1:amd64 (1:1.1.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up libuv1:amd64 (1.44.2-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libjbig2dec0:amd64 (0.19-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libteckit0:amd64 (2.5.11+ds1-1+b1) ... 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Setting up liblapack-dev:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up pkg-config:amd64 (1.8.1-1) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up libx265-199:amd64 (3.5-2+b1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libllvm14:amd64 (1:14.0.6-12) ... Setting up libgvpr2:amd64 (2.42.2-7+b3) ... Setting up dwz (0.15-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.2+b1) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libcurl4:amd64 (7.88.1-10+deb12u4) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libhwloc-dev:amd64 (2.9.0-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libfftw3-dev:amd64 (3.3.10-1) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up libibverbs1:amd64 (44.0-2) ... Setting up libxcb1-dev:amd64 (1.15-1) ... Setting up libxpm4:amd64 (1:3.5.12-1.1+deb12u1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up openssh-client (1:9.2p1-2+deb12u1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libheif1:amd64 (1.15.1-1) ... Setting up libx11-dev:amd64 (2:1.8.4-2+deb12u2) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libclang1-14 (1:14.0.6-12) ... Setting up libpaper-utils (1.1.29) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:amd64 (525.85.05-3~deb12u1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libnl-route-3-dev:amd64 (3.7.0-0.2+b1) ... Setting up sphinx-common (5.3.0-4) ... Setting up libclang-cpp14 (1:14.0.6-12) ... Setting up libgraphicsmagick-q16-3 (1.4+really1.3.40-4) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libcups2:amd64 (2.4.2-3+deb12u5) ... Setting up cmake (3.25.1-1) ... Setting up tex-gyre (20180621-6) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up python3.11 (3.11.2-6) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up libxmu6:amd64 (2:1.1.3-3) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up graphicsmagick (1.4+really1.3.40-4) ... Setting up preview-latex-style (12.2-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libxaw7:amd64 (2:1.0.14-1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up libibverbs-dev:amd64 (44.0-2) ... Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up doxygen (1.9.4-4) ... Setting up python3-packaging (23.0-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up python3-idna (3.3-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up libgs10-common (10.0.0~dfsg-11+deb12u2) ... Setting up libpmix2:amd64 (4.2.2-1+deb12u1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-charset-normalizer (3.0.1-2) ... Setting up fontconfig-config (2.14.1-4) ... Setting up python3-alabaster (0.7.12-1) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libpmix-dev:amd64 (4.2.2-1+deb12u1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libgs10:amd64 (10.0.0~dfsg-11+deb12u2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up mpi-default-bin (1.14) ... Setting up ghostscript (10.0.0~dfsg-11+deb12u2) ... Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libgd3:amd64 (2.3.3-9) ... Setting up texlive-binaries (2022.20220321.62855-5.1+deb12u1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up libopenmpi-dev:amd64 (4.1.4-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up texlive-base (2022.20230122-3) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up mscgen (0.20-14) ... Setting up texlive-latex-base (2022.20230122-3) ... Setting up texlive-latex-recommended (2022.20230122-3) ... Setting up libgvc6 (2.42.2-7+b3) ... Setting up texlive-pictures (2022.20230122-3) ... Setting up mpi-default-dev (1.14) ... Setting up texlive-fonts-recommended (2022.20230122-3) ... Setting up graphviz (2.42.2-7+b3) ... Setting up texlive-latex-extra (2022.20230122-4) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up python3-sphinx (5.3.0-4) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2889789/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bookworm I: user script /srv/workspace/pbuilder/2889789/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/gromacs-2022.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gromacs_2022.5-2_source.changes dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2022.5-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh_testdir dh_testroot dh_clean build-basic build-mpi build-manual build/ rm -rf admin/containers/__pycache__/scripted_gmx_docker_builds.cpython-3[91]*.pyc \ admin/containers/__pycache__/utility.cpython-3[91]*.pyc \ docs/__pycache__/gmxsphinx.cpython-3[91]*.pyc \ docs/doxygen/__pycache__/ debian/rules binary dh_testdir (mkdir -p build/basic; cd build/basic; cmake \ /build/reproducible-path/gromacs-2022.5 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2022.5-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_X11=ON -DGMX_INSTALL_LEGACY_API=ON ) -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Python3_LIBRARIES Development Development.Module Development.Embed) (found suitable version "3.11.2", minimum required is "3.7") -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.8.0", minimum required is "1.5") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "5.3.0", minimum required is "1.6.1") found components: pygments -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.11.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2022.5/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/reproducible-path/gromacs-2022.5 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2022.5-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=OFF -DGMX_X11=ON -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Python3_LIBRARIES Development Development.Module Development.Embed) (found suitable version "3.11.2", minimum required is "3.7") -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.8.0", minimum required is "1.5") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "5.3.0", minimum required is "1.6.1") found components: pygments -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.11.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2022.5/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2022.5 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2022.5-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DMPIEXEC="/usr/bin/mpiexec" ) -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Python3_LIBRARIES Development Development.Module Development.Embed) (found suitable version "3.11.2", minimum required is "3.7") -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 4.1.4 -- Using default binary suffix: "_mpi" -- Using default library suffix: "_mpi" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.8.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "5.3.0", minimum required is "1.6.1") found components: pygments -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.11.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2022.5/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2022.5 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2022.5-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMXAPI=OFF -DGMX_SIMD=SSE4.1 -DGMX_MPI=ON -DGMX_X11=OFF -DMPIEXEC="/usr/bin/mpiexec" -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Python3_LIBRARIES Development Development.Module Development.Embed) (found suitable version "3.11.2", minimum required is "3.7") -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 4.1.4 -- Using default binary suffix: "_mpi_d" -- Using default library suffix: "_mpi_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "2.8.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so - found -- Performing Test C_msse4_1_FLAG_ACCEPTED -- Performing Test C_msse4_1_FLAG_ACCEPTED - Success -- Performing Test C_msse4_1_COMPILE_WORKS -- Performing Test C_msse4_1_COMPILE_WORKS - Success -- Performing Test CXX_msse4_1_FLAG_ACCEPTED -- Performing Test CXX_msse4_1_FLAG_ACCEPTED - Success -- Performing Test CXX_msse4_1_COMPILE_WORKS -- Performing Test CXX_msse4_1_COMPILE_WORKS - Success -- Enabling SSE4.1 SIMD instructions using CXX flags: -msse4.1 -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "5.3.0", minimum required is "1.6.1") found components: pygments -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.11.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done -- Generating done -- Build files have been written to: /build/reproducible-path/gromacs-2022.5/build/mpi-dp touch configure-stamp dh_testdir /usr/bin/make -j15 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2022.5 -B/build/reproducible-path/gromacs-2022.5/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2022.5/build/basic/CMakeFiles /build/reproducible-path/gromacs-2022.5/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/selection /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs 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/usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2022.5-Debian_2022.5_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2022.5 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2022.5/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2022.5/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2022.5-2 -P /build/reproducible-path/gromacs-2022.5/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/include 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'/build/reproducible-path/gromacs-2022.5/build/basic' [ 4%] Built target thread_mpi [ 4%] Built target mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 6%] Built target view_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 8%] Built target linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 8%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 10%] Built target tng_io_obj /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 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CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 12%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2022.5/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2022.5/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs 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src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/futil.cpp In file included from /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/binaryinformation.cpp:74: /build/reproducible-path/gromacs-2022.5/build/basic/src/include/buildinfo.h:73: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.8.0" | In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/binaryinformation.cpp:60: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.9.0" | cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/init.cpp cd 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include 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-std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include 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-std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/coordinatetransformation.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/veccompare.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/boxutilities.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/manager.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/splineutil.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/decidegpuusage.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/decidesimulationworkload.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/findallgputasks.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/reportgpuusage.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/resourcedivision.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/taskassignment.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && 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src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/transformationcoordinate.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs 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-I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/resall.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tomorse.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/expfit.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/integrate.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd 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src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/dataframe.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/datamodulemanager.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/dataproxy.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/modules/average.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/coordinatefile.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadaptercontainer.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/outputselector.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/trjconv.cpp cd 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/broadcaststructs.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/constr.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/stat.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/biassharing.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfitting.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/manage_threading.cpp cd 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/identifyavx512fmaunits.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/runner.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ 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/build/reproducible-path/gromacs-2022.5/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/libxdrf.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/timecontrol.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/evaluate.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/indexutil.cpp In file included from /usr/include/c++/12/vector:64, from /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.h:40, from /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:39: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = float; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateKineticEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateKineticEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = float; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = float; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = float; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = float; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31, inlined from 'int do_cpte_nmatrix(XDR*, Enum, int, int, real**, FILE*) [with Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:1002:55: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int do_cpte_nmatrix(XDR*, Enum, int, int, real**, FILE*) [with Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = float; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullGroupEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullGroupEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/mempool.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/nbsearch.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = float; _Alloc = gmx::Allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = gmx::Allocator; Enum = StateEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = gmx::Allocator; Enum = StateEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = float; _Alloc = gmx::Allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEnergyEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEnergyEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateKineticEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateKineticEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/params.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selhelp.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selmethod.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selvalue.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2022.5/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.7.0.0 ../../lib/libgromacs.so.7 ../../lib/libgromacs.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 95%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/share/template /build/reproducible-path/gromacs-2022.5/build/basic 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api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/virials.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 95%] Built target gmx cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include 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/build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 97%] Built target template cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o ../../lib/libgromacs.so.7.0.0 /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lm cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/samples /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/samples /build/reproducible-path/gromacs-2022.5/build/basic 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/tmpi_malloc.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c 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-I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/mdrun.cpp [ 0%] Built target release-version-info make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/gmx_arpack.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include 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CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem 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/usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem 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-fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 12%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2022.5/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2022.5/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/futil.cpp In file included from /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/binaryinformation.cpp:74: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include/buildinfo.h:73: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.8.0" | In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/binaryinformation.cpp:60: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.9.0" | cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/init.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/logger.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/stringstream.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/stringutil.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/sycl_version_information.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/cmdlinemodulemanager.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/veccompare.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/vecdump.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/threaded_force_buffer.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/forcetable.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && 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-I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullcoordexpressionparser.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/simd/support.cpp.o -MF CMakeFiles/libgromacs.dir/simd/support.cpp.o.d -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/support.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_hydorder.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_saxs.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/nrama.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/h_db.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/toputil.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/integrate.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/manyautocorrelation.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/polynomials.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/statistics.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setforces.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setprecision.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/mk_angndx.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/broadcaststructs.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/freeenergyparameters.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/resethandler.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/correlationgrid.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/correlationhistory.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/correlationtensor.cpp cd 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cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/ewald_utils.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/long_range_correction.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/parallel_3dfft.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/gpu_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/gpu_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/gpu_3dfft.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/gpu_3dfft.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/fft_fftw3.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/gpu_utils.cpp cd 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/identifyavx512fmaunits.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -MF CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/filetypes.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/g96io.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/libxdrf.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/mrcserializer.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/mtxio.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/oenv.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tngio.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/trrio.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/trxio.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/writeps.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/position.cpp In file included from /usr/include/c++/12/vector:64, from /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.h:40, from /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:39: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullGroupEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullGroupEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/scanner_internal.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31, inlined from 'int do_cpte_nmatrix(XDR*, Enum, int, int, real**, FILE*) [with Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:1002:55: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int do_cpte_nmatrix(XDR*, Enum, int, int, real**, FILE*) [with Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selection.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = gmx::Allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = gmx::Allocator; Enum = StateEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = gmx::Allocator; Enum = StateEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = gmx::Allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEnergyEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEnergyEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateKineticEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateKineticEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectioncollection.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selhelp.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 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src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_distance.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_insolidangle.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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-std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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/usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.7.0.0 ../../lib/libgromacs_d.so.7 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 97%] Built target libgromacs /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib && 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/build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include 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/build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o ../../lib/libgromacs_d.so.7.0.0 /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -lm cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory 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/build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -std=c++17 -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2022.5/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2022.5/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2022.5/build/basic-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -j15 -C build/basic tests make[1]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2022.5 -B/build/reproducible-path/gromacs-2022.5/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/cmake 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Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/external/googletest/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++17 -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c 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/build/reproducible-path/gromacs-2022.5/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend [ 5%] Built target linearalgebra make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering 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api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 63%] Built target argon-forces-integration [ 63%] Built target methane-water-integration cd /build/reproducible-path/gromacs-2022.5/build/basic/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.11.0 -o ../../../../lib/libgtest.so.1.11.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2022.5/build/basic/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 63%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/external/googletest/googlemock /build/reproducible-path/gromacs-2022.5/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -I/build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++17 -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF 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'/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/alignedallocator.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/terminationhelper.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.7.0.0 ../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 64%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 64%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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-DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 64%] Built target testutils-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 64%] Built target nblib_test_infrastructure /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 64%] Built target applied_forces-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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-DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests/biasstate.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 64%] Built target nbnxm-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 64%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 64%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2022.5/build/basic 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-I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/device_availability.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF 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/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include 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-fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/device_stream_manager.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 66%] Built target domdec-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/ebin.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 66%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include 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-fopenmp -std=c++17 -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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/usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include 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-MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 68%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/options/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/message_string_collector.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" 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/build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/freeenergyparameters.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/path.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/range.cpp.o -MF CMakeFiles/utility-test.dir/range.cpp.o.d -o CMakeFiles/utility-test.dir/range.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/range.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. 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-I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c 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-I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF 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-DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tables/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 70%] Built target hardware-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include 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src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -MF CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o.d -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 70%] Built target mdspan-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/timing/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/timing/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -MF CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/typecasts.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 70%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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'/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock 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/build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 71%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" 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"CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 72%] Built target utility-test cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 72%] Built target pbcutil-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/compat/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/compat/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 72%] Built target timing-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/compat/tests/pointers.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lmuparser -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 [ 72%] Built target taskassignment-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/option.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 72%] Built target pull-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests 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-I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include 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-I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests/mtop.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. 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-I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 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-I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF 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'/build/reproducible-path/gromacs-2022.5/build/basic' [ 74%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/scalar_util.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 75%] Built target mdlib-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 75%] Built target table-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include 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make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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/usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E 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make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 77%] Built target mdtypes-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/checkpoint.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 78%] Built target correlations-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests 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src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 79%] Built target gmxana-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 79%] Built target energyanalysis-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/densityfittingmodule.cpp [ 79%] Built target pdb2gmx2-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_integer.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 81%] Built target pdb2gmx3-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/multiple_time_stepping.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/mrcserializer.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 82%] Built target topology-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem 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CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 82%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/selectioncollection.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 82%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers 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/build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd4.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd4_floatingpoint.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 82%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/multisim.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 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/build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 82%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 82%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include 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-I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat 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/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 83%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/replicaexchange_equivalence.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 85%] Built target options-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/rerun.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/tngio.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/settimestep.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 86%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic 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-I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest 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"CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 87%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/build.make 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/periodicactions.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 87%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 87%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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-DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/testmodule.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 89%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 89%] Built target mdrun-test cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/periodicactions_coupling.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 89%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 89%] Built target mdrun-non-integrator-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 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-I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/box.cpp /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/tpr.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 89%] Built target mdrun-fep-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/periodicactions_constraints.cpp In file included from /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include/gtest/gtest.h:60, from /build/reproducible-path/gromacs-2022.5/api/nblib/tests/tpr.cpp:43: /build/reproducible-path/gromacs-2022.5/api/nblib/tests/tpr.cpp: In member function 'virtual void nblib::test::TprReaderTest_Spc2Reads_Test::TestBody()': /build/reproducible-path/gromacs-2022.5/api/nblib/tests/tpr.cpp:91:48: warning: ignoring return value of 'std::vector<_Tp, _Alloc>::size_type std::vector<_Tp, _Alloc>::size() const [with _Tp = gmx::BasicVector; _Alloc = std::allocator >; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 91 | EXPECT_NO_THROW(tprReader.coordinates_.size()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/12/vector:64, from /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include/gtest/gtest.h:58: /usr/include/c++/12/bits/stl_vector.h:987:7: note: declared here 987 | size() const _GLIBCXX_NOEXCEPT | ^~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-mpi-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 89%] Built target mdrun-mpi-coordination-basic-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/bondtypes.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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/build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 90%] Built target mdrun-mpi-coordination-coupling-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/util/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/util/tests /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/util/tests/setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a 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-I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 90%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/particletype.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 90%] Built target mdrun-simulator-comparison-test cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/gmxcalculator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 90%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd 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/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external 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/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 91%] Built target mdrun-vsites-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/simstate.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/helpers.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 91%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 91%] Built target mdrun-mpi-coordination-constraints-test cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/listedtesthelpers.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 93%] Built target selection-test cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlineparser.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 [ 94%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/kernels.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 94%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/arraydata.cpp [ 94%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/virials.cpp.o -MF CMakeFiles/nblib-setup-test.dir/virials.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/virials.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 ../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/average.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 94%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 95%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 95%] Built target commandline-test In member function 'virtual void {anonymous}::UnionFinderTest_WorksEmpty_Test::TestBody()': cc1plus: warning: iteration 2147483648 invokes undefined behavior [-Waggressive-loop-optimizations] In file included from /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/unionfind.cpp:43: In member function 'std::vector gmx::UnionFinder::allSizes()', inlined from 'virtual void {anonymous}::UnionFinderTest_WorksEmpty_Test::TestBody()' at /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/unionfind.cpp:60:5: /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/unionfind.h:118:27: note: within this loop 118 | for (int i = 0; i < count; ++i) | ~~^~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 97%] Built target trajectoryanalysis-test cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 ../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [ 98%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build cd /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 ../../../../lib/libgromacs.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a [ 98%] Built target nblib-tests make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [100%] Built target nblib-listed-forces-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' cd /build/reproducible-path/gromacs-2022.5/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic /build/reproducible-path/gromacs-2022.5/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2022.5/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' make[1]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2022.5/build/basic/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2022.5/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2022.5/build/basic/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2022.5/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2022.5/build/basic/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2022.5/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: NbLibListedForcesTests 1: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/NbLibListedForcesTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/listed_forces/tests 1: Test timeout computed to be: 600 1: [==========] Running 44 tests from 22 test suites. 1: [----------] Global test environment set-up. 1: [----------] 8 tests from NBlibTest 1: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 1: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 1: [ RUN ] NBlibTest.BondTypesLessThanWorks 1: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 1: [ RUN ] NBlibTest.CanSplitListedWork 1: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 1: [ RUN ] NBlibTest.ListedForceBuffer 1: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 1: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 1: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (4 ms) 1: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 1: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (16 ms) 1: [ RUN ] NBlibTest.EndToEndListedComparison 1: [ OK ] NBlibTest.EndToEndListedComparison (21 ms) 1: [ RUN ] NBlibTest.shiftForcesAreCorrect 1: [ OK ] NBlibTest.shiftForcesAreCorrect (37 ms) 1: [----------] 8 tests from NBlibTest (80 ms total) 1: 1: [----------] 1 test from Kernels 1: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 1: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 1: [----------] 1 test from Kernels (0 ms total) 1: 1: [----------] 1 test from FourCenter 1: [ RUN ] FourCenter.ListedForcesProperDihedralTest 1: [ OK ] FourCenter.ListedForcesProperDihedralTest (2 ms) 1: [----------] 1 test from FourCenter (2 ms total) 1: 1: [----------] 7 tests from ThreeCenter 1: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 1: [ OK ] ThreeCenter.ListedForcesG96AngleTest (1 ms) 1: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 1: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (1 ms) 1: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 1: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 1: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 1: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (2 ms) 1: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 1: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 1: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 1: [----------] 7 tests from ThreeCenter (8 ms total) 1: 1: [----------] 5 tests from TwoCenter 1: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 1: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 1: [ RUN ] TwoCenter.ListedForcesG96BondTest 1: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 1: [ RUN ] TwoCenter.ListedForcesCubicBondTest 1: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 1: [ RUN ] TwoCenter.ListedForcesMorseBondTest 1: [ OK ] TwoCenter.ListedForcesMorseBondTest (1 ms) 1: [ RUN ] TwoCenter.ListedForcesFeneBondTest 1: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 1: [----------] 5 tests from TwoCenter (3 ms total) 1: 1: [----------] 5 tests from ListedExampleData 1: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 1: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 1: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 1: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 1: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 1: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 1: [ RUN ] ListedExampleData.CanReduceForces 1: [ OK ] ListedExampleData.CanReduceForces (0 ms) 1: [ RUN ] ListedExampleData.CanReduceEnergies 1: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 1: [----------] 5 tests from ListedExampleData (2 ms total) 1: 1: [----------] 1 test from LinearChainDataFixture 1: [ RUN ] LinearChainDataFixture.Multithreading 1: [ OK ] LinearChainDataFixture.Multithreading (29 ms) 1: [----------] 1 test from LinearChainDataFixture (29 ms total) 1: 1: [----------] 2 tests from ListedShims 1: [ RUN ] ListedShims.ParameterConversion 1: [ OK ] ListedShims.ParameterConversion (0 ms) 1: [ RUN ] ListedShims.GmxToNblibConversion 1: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 1: [----------] 2 tests from ListedShims (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 1: 1: [----------] 1 test from ListedTransformations 1: [ RUN ] ListedTransformations.SortInteractionIndices 1: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 1: [----------] 1 test from ListedTransformations (0 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 44 tests from 22 test suites ran. (127 ms total) 1: [ PASSED ] 44 tests. 1/81 Test #1: NbLibListedForcesTests ......................... Passed 0.35 sec test 2 Start 2: NbLibSamplesTestArgon 2: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/argon-forces-integration 2: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/samples 2: Test timeout computed to be: 1500 2: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 2: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 2: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 2: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 2/81 Test #2: NbLibSamplesTestArgon .......................... Passed 0.12 sec test 3 Start 3: NbLibSamplesTestMethaneWater 3: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/methane-water-integration 3: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/samples 3: Test timeout computed to be: 1500 3: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 3: final position of particle 9: x 77.358398 y 5.324913 z -80.600098 3/81 Test #3: NbLibSamplesTestMethaneWater ................... Passed 0.14 sec test 4 Start 4: NbLibUtilTests 4: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/NbLibUtilTests.xml" 4: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/util/tests 4: Test timeout computed to be: 30 4: [==========] Running 16 tests from 2 test suites. 4: [----------] Global test environment set-up. 4: [----------] 6 tests from NBlibTest 4: [ RUN ] NBlibTest.isRealValued 4: [ OK ] NBlibTest.isRealValued (0 ms) 4: [ RUN ] NBlibTest.checkNumericValuesHasNan 4: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 4: [ RUN ] NBlibTest.checkNumericValuesHasInf 4: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 4: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 4: Velocities were taken from a Maxwell distribution at 300 K 4: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 4: [ RUN ] NBlibTest.generateVelocitySize 4: Velocities were taken from a Maxwell distribution at 300 K 4: [ OK ] NBlibTest.generateVelocitySize (0 ms) 4: [ RUN ] NBlibTest.generateVelocityCheckNumbers 4: Velocities were taken from a Maxwell distribution at 300 K 4: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 4: [----------] 6 tests from NBlibTest (0 ms total) 4: 4: [----------] 10 tests from NblibTraitsUtils 4: [ RUN ] NblibTraitsUtils.FuseTwo 4: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 4: [ RUN ] NblibTraitsUtils.Fuse 4: [ OK ] NblibTraitsUtils.Fuse (0 ms) 4: [ RUN ] NblibTraitsUtils.Repeat 4: [ OK ] NblibTraitsUtils.Repeat (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTuple1 4: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTuple2 4: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 4: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 4: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 4: [ RUN ] NblibTraitsUtils.Contains 4: [ OK ] NblibTraitsUtils.Contains (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 4: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 4: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 4: [----------] 10 tests from NblibTraitsUtils (0 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 16 tests from 2 test suites ran. (0 ms total) 4: [ PASSED ] 16 tests. 4/81 Test #4: NbLibUtilTests ................................. Passed 0.06 sec test 5 Start 5: NbLibSetupTests 5: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/NbLibSetupTests.xml" 5: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests 5: Test timeout computed to be: 600 5: [==========] Running 56 tests from 3 test suites. 5: [----------] Global test environment set-up. 5: [----------] 41 tests from NBlibTest 5: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 5: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 5: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 5: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 5: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 5: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 5: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 5: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 5: [ RUN ] NBlibTest.CubicBoxWorks 5: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 5: [ RUN ] NBlibTest.BoxEqual 5: [ OK ] NBlibTest.BoxEqual (0 ms) 5: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 5: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 5: [ RUN ] NBlibTest.CanMergeInteractions 5: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 5: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 5: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 5: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 5: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 5: [ RUN ] NBlibTest.PbcHolderWorks 5: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 5: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 5: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 5: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 5: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 5: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 5: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 5: [ RUN ] NBlibTest.AtWorks 5: [ OK ] NBlibTest.AtWorks (0 ms) 5: [ RUN ] NBlibTest.AtThrows 5: [ OK ] NBlibTest.AtThrows (0 ms) 5: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 5: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 5: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 5: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 5: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 5: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 5: [ RUN ] NBlibTest.CanAddInteractions 5: [ OK ] NBlibTest.CanAddInteractions (0 ms) 5: [ RUN ] NBlibTest.CanAddUreyBradley 5: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 5: [ RUN ] NBlibTest.TopologyHasNumParticles 5: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 5: [ RUN ] NBlibTest.TopologyHasCharges 5: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 5: [ RUN ] NBlibTest.TopologyHasMasses 5: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 5: [ RUN ] NBlibTest.TopologyHasParticleTypes 5: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 5: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 5: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 5: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 5: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 5: [ RUN ] NBlibTest.TopologyHasExclusions 5: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 5: [ RUN ] NBlibTest.TopologyHasSequencing 5: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 5: [ RUN ] NBlibTest.TopologyCanAggregateBonds 5: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 5: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 5: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 5: [ RUN ] NBlibTest.TopologySequenceIdThrows 5: No particle O-Atom in residue SOL in molecule SOL found 5: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 5: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 5: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 5: [ RUN ] NBlibTest.TopologyListedInteractions 5: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 5: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 5: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 5: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 5: No particle Iron in residue SOL in molecule SOL found 5: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 5: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 5: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 5: [----------] 41 tests from NBlibTest (2 ms total) 5: 5: [----------] 14 tests from NbnxmSetupTest 5: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 5: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 5: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 5: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 5: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 5: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 5: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 5: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 5: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 5: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 5: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 5: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (4 ms) 5: [ RUN ] NbnxmSetupTest.updateForcerecWorks 5: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 5: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 5: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 5: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 5: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 5: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 5: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 5: [----------] 14 tests from NbnxmSetupTest (5 ms total) 5: 5: [----------] 1 test from VirialsTest 5: [ RUN ] VirialsTest.computeVirialTensorWorks 5: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 5: [----------] 1 test from VirialsTest (0 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 56 tests from 3 test suites ran. (8 ms total) 5: [ PASSED ] 56 tests. 5/81 Test #5: NbLibSetupTests ................................ Passed 0.42 sec test 6 Start 6: NbLibTprTests 6: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/NbLibTprTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests 6: Test timeout computed to be: 30 6: [==========] Running 4 tests from 1 test suite. 6: [----------] Global test environment set-up. 6: [----------] 4 tests from TprReaderTest 6: [ RUN ] TprReaderTest.SimDBTprIsCreated 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Number of degrees of freedom in T-Coupling group System is 33.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 6: NVE simulation: will use the initial temperature of 68.810 K for 6: determining the Verlet buffer size 6: 6: 6: There were 3 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 6: Generated 1 of the 1 non-bonded parameter combinations 6: 6: Excluding 1 bonded neighbours molecule type 'Argon' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.SimDBTprIsCreated (736 ms) 6: [ RUN ] TprReaderTest.Spc2Reads 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Generating 1-4 interactions: fudge = 0.5 6: Number of degrees of freedom in T-Coupling group System is 9.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: NVE simulation: will use the initial temperature of 2573.591 K for 6: determining the Verlet buffer size 6: 6: 6: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: You are using a plain Coulomb cut-off, which might produce artifacts. 6: You might want to consider using PME electrostatics. 6: 6: 6: 6: There were 4 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 6: Generated 3 of the 3 non-bonded parameter combinations 6: 6: Generated 3 of the 3 1-4 parameter combinations 6: 6: Excluding 2 bonded neighbours molecule type 'SOL' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.Spc2Reads (96 ms) 6: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Number of degrees of freedom in T-Coupling group System is 33.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 6: NVE simulation: will use the initial temperature of 68.810 K for 6: determining the Verlet buffer size 6: 6: 6: There were 3 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 6: Generated 1 of the 1 non-bonded parameter combinations 6: 6: Excluding 1 bonded neighbours molecule type 'Argon' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (75 ms) 6: [ RUN ] TprReaderTest.FCfromTprDataWorks 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Number of degrees of freedom in T-Coupling group System is 33.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 6: NVE simulation: will use the initial temperature of 68.810 K for 6: determining the Verlet buffer size 6: 6: 6: There were 3 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 6: Generated 1 of the 1 non-bonded parameter combinations 6: 6: Excluding 1 bonded neighbours molecule type 'Argon' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.FCfromTprDataWorks (72 ms) 6: [----------] 4 tests from TprReaderTest (980 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 4 tests from 1 test suite ran. (1135 ms total) 6: [ PASSED ] 4 tests. 6/81 Test #6: NbLibTprTests .................................. Passed 1.19 sec test 7 Start 7: NbLibIntegrationTests 7: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/NbLibIntegrationTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 20 tests from 1 test suite. 7: [----------] Global test environment set-up. 7: [----------] 20 tests from NBlibTest 7: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 7: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 7: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 7: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 7: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 7: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (16 ms) 7: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 7: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (1 ms) 7: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 7: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 7: [ RUN ] NBlibTest.ExpectedNumberOfForces 7: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 7: [ RUN ] NBlibTest.CanIntegrateSystem 7: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 7: [ RUN ] NBlibTest.UpdateChangesForces 7: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 7: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 7: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (4 ms) 7: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 7: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (7 ms) 7: [ RUN ] NBlibTest.CanConstructSimulationState 7: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 7: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 7: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 7: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 7: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 7: [ RUN ] NBlibTest.SimulationStateCanMove 7: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 7: [ RUN ] NBlibTest.SimulationStateCanAssign 7: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 7: [ RUN ] NBlibTest.SimulationStateHasBox 7: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 7: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 7: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 7: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 7: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 7: [----------] 20 tests from NBlibTest (36 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 20 tests from 1 test suite ran. (36 ms total) 7: [ PASSED ] 20 tests. 7/81 Test #7: NbLibIntegrationTests .......................... Passed 0.08 sec test 8 Start 8: NbLibIntegratorTests 8: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/NbLibIntegratorTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/api/nblib/tests 8: Test timeout computed to be: 600 8: [==========] Running 1 test from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 1 test from NBlibTest 8: [ RUN ] NBlibTest.IntegratorWorks 8: [ OK ] NBlibTest.IntegratorWorks (0 ms) 8: [----------] 1 test from NBlibTest (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 1 test from 1 test suite ran. (0 ms total) 8: [ PASSED ] 1 test. 8/81 Test #8: NbLibIntegratorTests ........................... Passed 0.07 sec test 9 Start 9: TestUtilsUnitTests 9: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/testutils/tests 9: Test timeout computed to be: 30 9: [==========] Running 59 tests from 5 test suites. 9: [----------] Global test environment set-up. 9: [----------] 10 tests from InteractiveTestHelperTest 9: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 9: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 9: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 9: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 9: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 9: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 9: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 9: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 9: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 9: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 9: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 9: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 9: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 9: [----------] 10 tests from InteractiveTestHelperTest (3 ms total) 9: 9: [----------] 34 tests from ReferenceDataTest 9: [ RUN ] ReferenceDataTest.HandlesSimpleData 9: [ OK ] ReferenceDataTest.HandlesSimpleData (8 ms) 9: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 9: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 9: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesStringBlockData 9: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesVectorData 9: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSequenceData 9: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 9: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesIncorrectData 9: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 9: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMissingData 9: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUncheckedData 9: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 9: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 9: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesAnys 9: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 9: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 9: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 9: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 9: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 9: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 9: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 9: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 9: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 9: [ OK ] ReferenceDataTest.HandlesEmptyStrings (4 ms) 9: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 9: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 9: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 9: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 9: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 9: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesReadingValues 9: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 9: [----------] 34 tests from ReferenceDataTest (23 ms total) 9: 9: [----------] 7 tests from FloatingPointDifferenceTest 9: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 9: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 9: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 9: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 9: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 9: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 9: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 9: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 9: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 9: 9: [----------] 4 tests from FloatingPointToleranceTest 9: [ RUN ] FloatingPointToleranceTest.UlpTolerance 9: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 9: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 9: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 9: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 9: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 9: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 9: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 9: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 9: 9: [----------] 4 tests from XvgTests 9: [ RUN ] XvgTests.CreateFile 9: [ OK ] XvgTests.CreateFile (0 ms) 9: [ RUN ] XvgTests.CheckMissing 9: [ OK ] XvgTests.CheckMissing (0 ms) 9: [ RUN ] XvgTests.CheckExtra 9: [ OK ] XvgTests.CheckExtra (0 ms) 9: [ RUN ] XvgTests.ReadIncorrect 9: [ OK ] XvgTests.ReadIncorrect (0 ms) 9: [----------] 4 tests from XvgTests (2 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 59 tests from 5 test suites ran. (29 ms total) 9: [ PASSED ] 59 tests. 9/81 Test #9: TestUtilsUnitTests ............................. Passed 0.09 sec test 10 Start 10: TestUtilsMpiUnitTests 10: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/testutils/tests 10: Test timeout computed to be: 30 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from MpiSelfTest 10: [ RUN ] MpiSelfTest.Runs 10: [ OK ] MpiSelfTest.Runs (21 ms) 10: [----------] 1 test from MpiSelfTest (22 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (22 ms total) 10: [ PASSED ] 1 test. 10/81 Test #10: TestUtilsMpiUnitTests .......................... Passed 0.06 sec test 11 Start 11: UtilityUnitTests 11: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/UtilityUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests 11: Test timeout computed to be: 30 11: [==========] Running 386 tests from 61 test suites. 11: [----------] Global test environment set-up. 11: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.Move 11: [ OK ] AllocatorTest/0.Move (0 ms) 11: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/0 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.Move 11: [ OK ] AllocatorTest/1.Move (0 ms) 11: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/1 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.Move 11: [ OK ] AllocatorTest/2.Move (0 ms) 11: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/2 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.Move 11: [ OK ] AllocatorTest/3.Move (0 ms) 11: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/3 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 11: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (2 ms) 11: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/4.Move 11: [ OK ] AllocatorTest/4.Move (0 ms) 11: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/4 (2 ms total) 11: 11: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 11: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/5.Move 11: [ OK ] AllocatorTest/5.Move (0 ms) 11: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/5 (0 ms total) 11: 11: [----------] 1 test from AllocatorUntypedTest 11: [ RUN ] AllocatorUntypedTest.Comparison 11: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 11: [----------] 1 test from AllocatorUntypedTest (0 ms total) 11: 11: [----------] 4 tests from EmptyArrayRefTest 11: [ RUN ] EmptyArrayRefTest.IsEmpty 11: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 11: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 11: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 11: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 11: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 11: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 11: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 11: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 11: 11: [----------] 1 test from EmptyConstArrayRefTest 11: [ RUN ] EmptyConstArrayRefTest.IsEmpty 11: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 11: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 11: 11: [----------] 2 tests from CStringUtilityTest 11: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 11: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 11: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 11: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 11: [----------] 2 tests from CStringUtilityTest (0 ms total) 11: 11: [----------] 2 tests from DefaultInitializationAllocator 11: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 11: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 11: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 11: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 11: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 11: 11: [----------] 4 tests from EnumerationHelpersTest 11: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 11: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 11: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 11: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 11: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 11: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 11: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 11: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 11: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 11: 11: [----------] 9 tests from FixedCapacityVectorTest 11: [ RUN ] FixedCapacityVectorTest.IsEmpty 11: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 11: [ RUN ] FixedCapacityVectorTest.PushWorks 11: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.PopWorks 11: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.ClearWorks 11: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 11: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.AtThrows 11: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 11: [ RUN ] FixedCapacityVectorTest.IteratorWorks 11: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 11: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 11: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 11: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 11: 11: [----------] 5 tests from InMemorySerializerTest 11: [ RUN ] InMemorySerializerTest.Roundtrip 11: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 11: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 11: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 11: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 11: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 11: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 11: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 11: [ RUN ] InMemorySerializerTest.SizeIsCorrect 11: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 11: [----------] 5 tests from InMemorySerializerTest (0 ms total) 11: 11: [----------] 4 tests from KeyValueTreeSerializerTest 11: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 11: [ OK ] KeyValueTreeSerializerTest.EmptyTree (14 ms) 11: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 11: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 11: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 11: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 11: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 11: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 11: [----------] 4 tests from KeyValueTreeSerializerTest (14 ms total) 11: 11: [----------] 6 tests from TreeValueTransformTest 11: [ RUN ] TreeValueTransformTest.SimpleTransforms 11: [ OK ] TreeValueTransformTest.SimpleTransforms (6 ms) 11: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 11: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 11: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 11: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 11: [ RUN ] TreeValueTransformTest.ObjectFromString 11: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 11: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 11: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (3 ms) 11: [ RUN ] TreeValueTransformTest.ScopedTransformRules 11: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 11: [----------] 6 tests from TreeValueTransformTest (11 ms total) 11: 11: [----------] 1 test from TreeValueTransformErrorTest 11: [ RUN ] TreeValueTransformErrorTest.ConversionError 11: [ OK ] TreeValueTransformErrorTest.ConversionError (27 ms) 11: [----------] 1 test from TreeValueTransformErrorTest (27 ms total) 11: 11: [----------] 9 tests from ListOfLists 11: [ RUN ] ListOfLists.EmptyListOfListsWorks 11: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 11: [ RUN ] ListOfLists.AppendWorks 11: [ OK ] ListOfLists.AppendWorks (0 ms) 11: [ RUN ] ListOfLists.EmptyListWorks 11: [ OK ] ListOfLists.EmptyListWorks (0 ms) 11: [ RUN ] ListOfLists.AppendAccessWorks 11: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 11: [ RUN ] ListOfLists.ClearWorks 11: [ OK ] ListOfLists.ClearWorks (0 ms) 11: [ RUN ] ListOfLists.OutOfRangeAccessThrows 11: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 11: [ RUN ] ListOfLists.FrontAndBackWork 11: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 11: [ RUN ] ListOfLists.ExtractsAndRestores 11: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 11: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 11: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 11: [----------] 9 tests from ListOfLists (0 ms total) 11: 11: [----------] 7 tests from LoggerTest 11: [ RUN ] LoggerTest.EmptyLoggerWorks 11: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 11: [ RUN ] LoggerTest.LogsToStream 11: [ OK ] LoggerTest.LogsToStream (0 ms) 11: [ RUN ] LoggerTest.LogsToFile 11: [ OK ] LoggerTest.LogsToFile (0 ms) 11: [ RUN ] LoggerTest.LevelFilteringWorks 11: [ OK ] LoggerTest.LevelFilteringWorks (11 ms) 11: [ RUN ] LoggerTest.LogsToMultipleStreams 11: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 11: [ RUN ] LoggerTest.LogsToMultipleFiles 11: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 11: [ RUN ] LoggerTest.LogsToStreamAndFile 11: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 11: [----------] 7 tests from LoggerTest (12 ms total) 11: 11: [----------] 4 tests from MDModulesNotifierTest 11: [ RUN ] MDModulesNotifierTest.AddConsumer 11: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 11: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 11: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 11: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 11: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 11: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 11: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 11: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 11: 11: [----------] 7 tests from MessageStringCollectorTest 11: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 11: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (7 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 11: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 11: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 11: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 11: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 11: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanMoveAssign 11: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 11: [----------] 7 tests from MessageStringCollectorTest (7 ms total) 11: 11: [----------] 1 test from PathTest 11: [ RUN ] PathTest.StripSourcePrefixWorks 11: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 11: [----------] 1 test from PathTest (0 ms total) 11: 11: [----------] 2 tests from PhysicalNodeCommunicatorTest 11: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 11: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 11: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 11: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 11: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 11: 11: [----------] 5 tests from Range 11: [ RUN ] Range.EmptyRangeWorks 11: [ OK ] Range.EmptyRangeWorks (0 ms) 11: [ RUN ] Range.NonEmptyRangeWorks 11: [ OK ] Range.NonEmptyRangeWorks (0 ms) 11: [ RUN ] Range.BeginEnd 11: [ OK ] Range.BeginEnd (0 ms) 11: [ RUN ] Range.IsInRangeWorks 11: [ OK ] Range.IsInRangeWorks (0 ms) 11: [ RUN ] Range.IteratorWorks 11: [ OK ] Range.IteratorWorks (0 ms) 11: [----------] 5 tests from Range (0 ms total) 11: 11: [----------] 7 tests from StringConvert 11: [ RUN ] StringConvert.NoResultFromEptyString 11: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 11: [ RUN ] StringConvert.ThreeFloatsSuccessfully 11: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 11: [ RUN ] StringConvert.OneIntSucessfully 11: [ OK ] StringConvert.OneIntSucessfully (0 ms) 11: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 11: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 11: [ RUN ] StringConvert.ThrowsWhenWrongSize 11: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 11: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 11: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 11: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 11: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 11: [----------] 7 tests from StringConvert (0 ms total) 11: 11: [----------] 7 tests from StringToEnumValueConverterTest 11: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 11: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 11: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 11: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 11: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 11: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 11: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 11: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 11: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 11: 11: [----------] 9 tests from StringUtilityTest 11: [ RUN ] StringUtilityTest.StartsWith 11: [ OK ] StringUtilityTest.StartsWith (0 ms) 11: [ RUN ] StringUtilityTest.EndsWith 11: [ OK ] StringUtilityTest.EndsWith (0 ms) 11: [ RUN ] StringUtilityTest.StripSuffixIfPresent 11: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 11: [ RUN ] StringUtilityTest.StripString 11: [ OK ] StringUtilityTest.StripString (0 ms) 11: [ RUN ] StringUtilityTest.SplitString 11: [ OK ] StringUtilityTest.SplitString (0 ms) 11: [ RUN ] StringUtilityTest.SplitDelimitedString 11: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 11: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 11: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 11: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 11: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 11: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 11: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 11: [----------] 9 tests from StringUtilityTest (0 ms total) 11: 11: [----------] 2 tests from FormatStringTest 11: [ RUN ] FormatStringTest.HandlesBasicFormatting 11: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 11: [ RUN ] FormatStringTest.HandlesLongStrings 11: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 11: [----------] 2 tests from FormatStringTest (0 ms total) 11: 11: [----------] 1 test from StringFormatterTest 11: [ RUN ] StringFormatterTest.HandlesBasicFormatting 11: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 11: [----------] 1 test from StringFormatterTest (0 ms total) 11: 11: [----------] 1 test from formatAndJoinTest 11: [ RUN ] formatAndJoinTest.Works 11: [ OK ] formatAndJoinTest.Works (0 ms) 11: [----------] 1 test from formatAndJoinTest (0 ms total) 11: 11: [----------] 1 test from JoinStringsTest 11: [ RUN ] JoinStringsTest.Works 11: [ OK ] JoinStringsTest.Works (0 ms) 11: [----------] 1 test from JoinStringsTest (0 ms total) 11: 11: [----------] 6 tests from ReplaceAllTest 11: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 11: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesNoMatches 11: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 11: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 11: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 11: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 11: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 11: [----------] 6 tests from ReplaceAllTest (0 ms total) 11: 11: [----------] 10 tests from TextLineWrapperTest 11: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 11: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 11: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 11: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 11: [ RUN ] TextLineWrapperTest.WrapsCorrectly 11: [ OK ] TextLineWrapperTest.WrapsCorrectly (3 ms) 11: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 11: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (3 ms) 11: [ RUN ] TextLineWrapperTest.HandlesIndent 11: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 11: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 11: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 11: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 11: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 11: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 11: [----------] 10 tests from TextLineWrapperTest (7 ms total) 11: 11: [----------] 3 tests from TemplateMPTest 11: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 11: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 11: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 11: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 11: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 11: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 11: [----------] 3 tests from TemplateMPTest (0 ms total) 11: 11: [----------] 6 tests from TextWriterTest 11: [ RUN ] TextWriterTest.WritesLines 11: [ OK ] TextWriterTest.WritesLines (0 ms) 11: [ RUN ] TextWriterTest.WritesLinesInParts 11: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 11: [ RUN ] TextWriterTest.WritesWrappedLines 11: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 11: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 11: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 11: [ RUN ] TextWriterTest.TracksNewlines 11: [ OK ] TextWriterTest.TracksNewlines (0 ms) 11: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 11: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 11: [----------] 6 tests from TextWriterTest (0 ms total) 11: 11: [----------] 1 test from TypeTraitsTest 11: [ RUN ] TypeTraitsTest.IsIntegralConstant 11: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 11: [----------] 1 test from TypeTraitsTest (0 ms total) 11: 11: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 11: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 11: 11: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 11: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 11: 11: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 11: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 11: 11: [----------] 11 tests from WithInputPaths/PathSearchTest 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 11: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 11: 11: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 11: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 386 tests from 61 test suites ran. (91 ms total) 11: [ PASSED ] 386 tests. 11: 11: YOU HAVE 1 DISABLED TEST 11: 11/81 Test #11: UtilityUnitTests ............................... Passed 0.16 sec test 12 Start 12: UtilityMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/utility/tests 12: Test timeout computed to be: 30 12: [==========] Running 2 tests from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 2 tests from PhysicalNodeCommunicatorTest 12: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 12: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 12: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 12: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms) 12: [----------] 2 tests from PhysicalNodeCommunicatorTest (1 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 2 tests from 1 test suite ran. (2 ms total) 12: [ PASSED ] 2 tests. 12/81 Test #12: UtilityMpiUnitTests ............................ Passed 0.05 sec test 13 Start 13: GmxlibTests 13: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/GmxlibTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxlib/nonbonded/tests 13: Test timeout computed to be: 30 13: [==========] Running 72 tests from 1 test suite. 13: [----------] Global test environment set-up. 13: [----------] 72 tests from NBInteraction/NonbondedFepTest 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (15 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (12 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (15 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (7 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (3 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (19 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (11 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (3 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (3 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (33 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (1 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (5 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (3 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (2 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (4 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (6 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (3 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (4 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 13: [----------] 72 tests from NBInteraction/NonbondedFepTest (170 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 72 tests from 1 test suite ran. (170 ms total) 13: [ PASSED ] 72 tests. 13/81 Test #13: GmxlibTests .................................... Passed 0.27 sec test 14 Start 14: MdlibUnitTest 14: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdlibUnitTest.xml" 14: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests 14: Test timeout computed to be: 30 14: [==========] Running 155 tests from 17 test suites. 14: [----------] Global test environment set-up. 14: [----------] 1 test from VerletBufferConstraintTest 14: [ RUN ] VerletBufferConstraintTest.EqualMasses 14: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 14: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 14: 14: [----------] 6 tests from CalcvirTest 14: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 14: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (18 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 14: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (4 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (11 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (3 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (4 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (3 ms) 14: [----------] 6 tests from CalcvirTest (47 ms total) 14: 14: [----------] 2 tests from PrEbinTest 14: [ RUN ] PrEbinTest.HandlesAverages 14: [ OK ] PrEbinTest.HandlesAverages (16 ms) 14: [ RUN ] PrEbinTest.HandlesEmptyAverages 14: [ OK ] PrEbinTest.HandlesEmptyAverages (3 ms) 14: [----------] 2 tests from PrEbinTest (20 ms total) 14: 14: [----------] 3 tests from EnergyDriftTracker 14: [ RUN ] EnergyDriftTracker.emptyWorks 14: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 14: [ RUN ] EnergyDriftTracker.onePointWorks 14: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 14: [ RUN ] EnergyDriftTracker.manyPointsWorks 14: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 14: [----------] 3 tests from EnergyDriftTracker (0 ms total) 14: 14: [----------] 4 tests from ShakeTest 14: [ RUN ] ShakeTest.ConstrainsOneBond 14: [ OK ] ShakeTest.ConstrainsOneBond (3 ms) 14: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 14: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 14: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 14: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 14: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 14: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 14: [----------] 4 tests from ShakeTest (3 ms total) 14: 14: [----------] 1 test from NullSignalTest 14: [ RUN ] NullSignalTest.NullSignallerWorks 14: [ OK ] NullSignalTest.NullSignallerWorks (3 ms) 14: [----------] 1 test from NullSignalTest (3 ms total) 14: 14: [----------] 7 tests from SignalTest 14: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 14: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 14: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 14: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 14: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 14: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 14: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 14: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 14: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 14: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 14: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 14: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 14: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 14: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 14: [----------] 7 tests from SignalTest (0 ms total) 14: 14: [----------] 13 tests from UpdateGroupsTest 14: [ RUN ] UpdateGroupsTest.WithEthaneUA 14: [ OK ] UpdateGroupsTest.WithEthaneUA (3 ms) 14: [ RUN ] UpdateGroupsTest.WithMethane 14: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 14: [ RUN ] UpdateGroupsTest.WithEthane 14: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 14: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 14: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 14: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 14: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 14: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 14: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 14: [ RUN ] UpdateGroupsTest.WithWaterFourSite 14: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 14: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 14: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 14: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 14: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 14: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 14: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 14: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 14: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 14: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 14: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 14: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 14: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 14: [----------] 13 tests from UpdateGroupsTest (5 ms total) 14: 14: [----------] 1 test from UpdateGroupsCog 14: [ RUN ] UpdateGroupsCog.ComputesCogs 14: [ OK ] UpdateGroupsCog.ComputesCogs (15 ms) 14: [----------] 1 test from UpdateGroupsCog (15 ms total) 14: 14: [----------] 2 tests from WholeMoleculeTransform 14: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 14: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (7 ms) 14: [ RUN ] WholeMoleculeTransform.HandlesReordering 14: [ OK ] WholeMoleculeTransform.HandlesReordering (3 ms) 14: [----------] 2 tests from WholeMoleculeTransform (11 ms total) 14: 14: [----------] 14 tests from WithParameters/ConstraintsTest 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (16 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (3 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (3 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (3 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (3 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (3 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (3 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (3 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (3 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (36 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (16 ms) 14: [----------] 14 tests from WithParameters/ConstraintsTest (112 ms total) 14: 14: [----------] 11 tests from WithParameters/EnergyOutputTest 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (43 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (1 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 14: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 14: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (22 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (12 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (7 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (26 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (1 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (6 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (11 ms) 14: [----------] 11 tests from WithParameters/EnergyOutputTest (149 ms total) 14: 14: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (17 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 14: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (18 ms total) 14: 14: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 14: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 14: 14: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 14: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 14: 14: [----------] 16 tests from WithParameters/LeapFrogTest 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (10 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (3 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (33 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (19 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (8 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (33 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (27 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (11 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (5 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (6 ms) 14: [----------] 16 tests from WithParameters/LeapFrogTest (168 ms total) 14: 14: [----------] 13 tests from WithParameters/SettleTest 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (5 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (1 ms) 14: [----------] 13 tests from WithParameters/SettleTest (18 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 155 tests from 17 test suites ran. (574 ms total) 14: [ PASSED ] 155 tests. 14/81 Test #14: MdlibUnitTest .................................. Passed 0.79 sec test 15 Start 15: AwhTest 15: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/AwhTest.xml" 15: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/awh/tests 15: Test timeout computed to be: 30 15: [==========] Running 21 tests from 8 test suites. 15: [----------] Global test environment set-up. 15: [----------] 3 tests from SerializationTest 15: [ RUN ] SerializationTest.CanSerializeDimParams 15: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 15: [ RUN ] SerializationTest.CanSerializeBiasParams 15: [ OK ] SerializationTest.CanSerializeBiasParams (12 ms) 15: [ RUN ] SerializationTest.CanSerializeAwhParams 15: [ OK ] SerializationTest.CanSerializeAwhParams (8 ms) 15: [----------] 3 tests from SerializationTest (20 ms total) 15: 15: [----------] 1 test from BiasTest 15: [ RUN ] BiasTest.DetectsCovering 15: [ OK ] BiasTest.DetectsCovering (44 ms) 15: [----------] 1 test from BiasTest (44 ms total) 15: 15: [----------] 1 test from biasGridTest 15: [ RUN ] biasGridTest.neighborhood 15: [ OK ] biasGridTest.neighborhood (1 ms) 15: [----------] 1 test from biasGridTest (1 ms total) 15: 15: [----------] 1 test from BiasSharingTest 15: [ RUN ] BiasSharingTest.SharingWorks 15: [ OK ] BiasSharingTest.SharingWorks (129 ms) 15: [----------] 1 test from BiasSharingTest (129 ms total) 15: 15: [----------] 1 test from BiasFepLambdaStateTest 15: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 15: [ OK ] BiasFepLambdaStateTest.DetectsCovering (7 ms) 15: [----------] 1 test from BiasFepLambdaStateTest (7 ms total) 15: 15: [----------] 8 tests from WithParameters/BiasTest 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (7 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (7 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (3 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (15 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (7 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (7 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (3 ms) 15: [----------] 8 tests from WithParameters/BiasTest (56 ms total) 15: 15: [----------] 2 tests from WithParameters/BiasStateTest 15: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 15: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (11 ms) 15: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 15: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 15: [----------] 2 tests from WithParameters/BiasStateTest (11 ms total) 15: 15: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (16 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (30 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (23 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (23 ms) 15: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (96 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 21 tests from 8 test suites ran. (369 ms total) 15: [ PASSED ] 21 tests. 15/81 Test #15: AwhTest ........................................ Passed 0.42 sec test 16 Start 16: DensityFittingAppliedForcesUnitTest 16: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/densityfitting/tests 16: Test timeout computed to be: 30 16: [==========] Running 18 tests from 4 test suites. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from DensityFittingTest 16: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 16: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (16 ms) 16: [ RUN ] DensityFittingTest.SingleAtom 16: [ OK ] DensityFittingTest.SingleAtom (91 ms) 16: [----------] 2 tests from DensityFittingTest (108 ms total) 16: 16: [----------] 7 tests from DensityFittingAmplitudeLookupTest 16: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 16: [ OK ] DensityFittingAmplitudeLookupTest.Unity (3 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 16: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 16: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 16: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 16: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 16: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 16: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 16: [----------] 7 tests from DensityFittingAmplitudeLookupTest (4 ms total) 16: 16: [----------] 1 test from DensityFittingForceProviderState 16: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 16: [ OK ] DensityFittingForceProviderState.RoundTripSaving (3 ms) 16: [----------] 1 test from DensityFittingForceProviderState (3 ms total) 16: 16: [----------] 8 tests from DensityFittingOptionsTest 16: [ RUN ] DensityFittingOptionsTest.DefaultParameters 16: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 16: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 16: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 16: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 16: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 16: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 16: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 16: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 16: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 16: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 16: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 16: [ RUN ] DensityFittingOptionsTest.KvtToInternal 16: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 16: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 16: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 16: [----------] 8 tests from DensityFittingOptionsTest (1 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 18 tests from 4 test suites ran. (117 ms total) 16: [ PASSED ] 18 tests. 16/81 Test #16: DensityFittingAppliedForcesUnitTest ............ Passed 0.16 sec test 17 Start 17: QMMMAppliedForcesUnitTest 17: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests 17: Test timeout computed to be: 30 17: [==========] Running 21 tests from 5 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from QMMMInputGeneratorTest 17: [ RUN ] QMMMInputGeneratorTest.CanConstruct 17: [ OK ] QMMMInputGeneratorTest.CanConstruct (8 ms) 17: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 17: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (12 ms) 17: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 17: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (3 ms) 17: [----------] 3 tests from QMMMInputGeneratorTest (24 ms total) 17: 17: [----------] 7 tests from QMMMTopologyPreprocessorTest 17: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 17: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 21.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to 1879023051 17: 17: Generated 10 of the 10 non-bonded parameter combinations 17: 17: Generated 10 of the 10 1-4 parameter combinations 17: 17: Excluding 2 bonded neighbours molecule type 'SOL' 17: Analysing residue names: 17: There are: 4 Water residues 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (47 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 21.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to 1541387007 17: 17: Generated 10 of the 10 non-bonded parameter combinations 17: 17: Generated 10 of the 10 1-4 parameter combinations 17: 17: Excluding 2 bonded neighbours molecule type 'SOL' 17: Analysing residue names: 17: There are: 4 Water residues 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (5 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 21.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to -2034238601 17: 17: Generated 10 of the 10 non-bonded parameter combinations 17: 17: Generated 10 of the 10 1-4 parameter combinations 17: 17: Excluding 2 bonded neighbours molecule type 'SOL' 17: Analysing residue names: 17: There are: 4 Water residues 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (18 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 63.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 17: NVE simulation: will use the initial temperature of 129.093 K for 17: determining the Verlet buffer size 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to -102304402 17: 17: Generated 2145 of the 2145 non-bonded parameter combinations 17: 17: Generated 2145 of the 2145 1-4 parameter combinations 17: 17: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 17: Analysing residue names: 17: There are: 3 Protein residues 17: Analysing Protein... 17: 17: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 17: 17: Calculated rlist for 1x1 atom pair-list as 1.013 nm, buffer size 0.013 nm 17: 17: Set rlist, assuming 4x4 atom pair-list, to 1.008 nm, buffer size 0.008 nm 17: 17: Note that mdrun will redetermine rlist based on the actual pair-list setup 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (111 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: 17: NOTE 2 [file unknown]: 17: You are using constraints on all bonds, whereas the forcefield has been 17: parametrized only with constraints involving hydrogen atoms. We suggest 17: using constraints = h-bonds instead, this will also improve performance. 17: 17: 17: NOTE 3 [file unknown]: 17: For energy conservation with LINCS, lincs_iter should be 2 or larger. 17: 17: 17: Number of degrees of freedom in T-Coupling group rest is 42.00 17: 17: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 17: NVE simulation: will use the initial temperature of 193.640 K for 17: determining the Verlet buffer size 17: 17: 17: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 5 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to 1878486511 17: 17: Generated 2145 of the 2145 non-bonded parameter combinations 17: 17: Generated 2145 of the 2145 1-4 parameter combinations 17: 17: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 17: 17: turning all bonds into constraints... 17: Analysing residue names: 17: There are: 3 Protein residues 17: Analysing Protein... 17: 17: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 17: 17: Calculated rlist for 1x1 atom pair-list as 1.015 nm, buffer size 0.015 nm 17: 17: Set rlist, assuming 4x4 atom pair-list, to 1.009 nm, buffer size 0.009 nm 17: 17: Note that mdrun will redetermine rlist based on the actual pair-list setup 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (35 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Number of degrees of freedom in T-Coupling group rest is 45.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to -209731731 17: 17: Generated 3 of the 6 non-bonded parameter combinations 17: 17: Excluding 3 bonded neighbours molecule type 'VSTEST' 17: 17: Cleaning up constraints and constant bonded interactions with virtual sites 17: Analysing residue names: 17: There are: 1 Other residues 17: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (53 ms) 17: [----------] 7 tests from QMMMTopologyPreprocessorTest (273 ms total) 17: 17: [----------] 9 tests from QMMMOptionsTest 17: [ RUN ] QMMMOptionsTest.DefaultParameters 17: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 17: [ RUN ] QMMMOptionsTest.OptionSetsActive 17: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 17: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 17: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 17: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 17: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 17: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 17: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 17: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 17: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (5 ms) 17: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 17: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 17: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 17: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 17: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 17: [ OK ] QMMMOptionsTest.CP2KInputProcessing (4 ms) 17: [----------] 9 tests from QMMMOptionsTest (10 ms total) 17: 17: [----------] 1 test from QMMMForceProviderTest 17: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 17: [ OK ] QMMMForceProviderTest.CanConstructOrNot (15 ms) 17: [----------] 1 test from QMMMForceProviderTest (15 ms total) 17: 17: [----------] 1 test from QMMMTest 17: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 17: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 17: [----------] 1 test from QMMMTest (0 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 21 tests from 5 test suites ran. (324 ms total) 17: [ PASSED ] 21 tests. 17/81 Test #17: QMMMAppliedForcesUnitTest ...................... Passed 0.37 sec test 18 Start 18: AppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/applied_forces/tests 18: Test timeout computed to be: 30 18: [==========] Running 3 tests from 1 test suite. 18: [----------] Global test environment set-up. 18: [----------] 3 tests from ElectricFieldTest 18: [ RUN ] ElectricFieldTest.Static 18: [ OK ] ElectricFieldTest.Static (2 ms) 18: [ RUN ] ElectricFieldTest.Oscillating 18: [ OK ] ElectricFieldTest.Oscillating (0 ms) 18: [ RUN ] ElectricFieldTest.Pulsed 18: [ OK ] ElectricFieldTest.Pulsed (0 ms) 18: [----------] 3 tests from ElectricFieldTest (3 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 3 tests from 1 test suite ran. (3 ms total) 18: [ PASSED ] 3 tests. 18/81 Test #18: AppliedForcesUnitTest .......................... Passed 0.04 sec test 19 Start 19: ListedForcesTest 19: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/ListedForcesTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/listed_forces/tests 19: Test timeout computed to be: 30 19: [==========] Running 132 tests from 9 test suites. 19: [----------] Global test environment set-up. 19: [----------] 24 tests from Bond/ListedForcesTest 19: [ RUN ] Bond/ListedForcesTest.Ifunc/0 19: [ OK ] Bond/ListedForcesTest.Ifunc/0 (14 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/1 19: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/2 19: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/3 19: [ OK ] Bond/ListedForcesTest.Ifunc/3 (1 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/4 19: [ OK ] Bond/ListedForcesTest.Ifunc/4 (1 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/5 19: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/6 19: [ OK ] Bond/ListedForcesTest.Ifunc/6 (2 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/7 19: [ OK ] Bond/ListedForcesTest.Ifunc/7 (1 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/8 19: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/9 19: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/10 19: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/11 19: [ OK ] Bond/ListedForcesTest.Ifunc/11 (1 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/12 19: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/13 19: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/14 19: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/15 19: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/16 19: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/17 19: [ OK ] Bond/ListedForcesTest.Ifunc/17 (1 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/18 19: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/19 19: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/20 19: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/21 19: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/22 19: [ OK ] Bond/ListedForcesTest.Ifunc/22 (5 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/23 19: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 19: [----------] 24 tests from Bond/ListedForcesTest (38 ms total) 19: 19: [----------] 33 tests from Angle/ListedForcesTest 19: [ RUN ] Angle/ListedForcesTest.Ifunc/0 19: [ OK ] Angle/ListedForcesTest.Ifunc/0 (1 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/1 19: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/2 19: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/3 19: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/4 19: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/5 19: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/6 19: [ OK ] Angle/ListedForcesTest.Ifunc/6 (1 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/7 19: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/8 19: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/9 19: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/10 19: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/11 19: [ OK ] Angle/ListedForcesTest.Ifunc/11 (1 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/12 19: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/13 19: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/14 19: [ OK ] Angle/ListedForcesTest.Ifunc/14 (1 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/15 19: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/16 19: [ OK ] Angle/ListedForcesTest.Ifunc/16 (1 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/17 19: [ OK ] Angle/ListedForcesTest.Ifunc/17 (1 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/18 19: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/19 19: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/20 19: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/21 19: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/22 19: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/23 19: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/24 19: [ OK ] Angle/ListedForcesTest.Ifunc/24 (1 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/25 19: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/26 19: [ OK ] Angle/ListedForcesTest.Ifunc/26 (1 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/27 19: [ OK ] Angle/ListedForcesTest.Ifunc/27 (1 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/28 19: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/29 19: [ OK ] Angle/ListedForcesTest.Ifunc/29 (1 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/30 19: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/31 19: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/32 19: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 19: [----------] 33 tests from Angle/ListedForcesTest (24 ms total) 19: 19: [----------] 18 tests from Dihedral/ListedForcesTest 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (1 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 19: [----------] 18 tests from Dihedral/ListedForcesTest (7 ms total) 19: 19: [----------] 12 tests from Polarize/ListedForcesTest 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 19: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 19: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 19: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (4 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 19: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 19: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 19: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 19: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 19: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 19: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 19: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 19: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (4 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 19: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (2 ms) 19: [----------] 12 tests from Polarize/ListedForcesTest (13 ms total) 19: 19: [----------] 18 tests from Restraints/ListedForcesTest 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 19: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 19: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 19: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 19: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 19: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 19: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 19: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 19: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 19: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 19: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (1 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 19: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 19: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 19: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 19: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 19: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 19: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 19: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 19: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 19: [----------] 18 tests from Restraints/ListedForcesTest (6 ms total) 19: 19: [----------] 3 tests from BondZeroLength/ListedForcesTest 19: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 19: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (4 ms) 19: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 19: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 19: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 19: [----------] 3 tests from BondZeroLength/ListedForcesTest (4 ms total) 19: 19: [----------] 3 tests from AngleZero/ListedForcesTest 19: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 19: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 19: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 19: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 19: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 19: 19: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (1 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (7 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (5 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 19: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (17 ms total) 19: 19: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 19: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (1 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 132 tests from 9 test suites ran. (114 ms total) 19: [ PASSED ] 132 tests. 19/81 Test #19: ListedForcesTest ............................... Passed 0.19 sec test 20 Start 20: NbnxmTests 20: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/NbnxmTests.xml" 20: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/nbnxm/tests 20: Test timeout computed to be: 30 20: [==========] Running 18 tests from 1 test suite. 20: [----------] Global test environment set-up. 20: [----------] 18 tests from KernelSetupTest 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 20: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 20: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 20: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 20: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 20: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 20: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 20: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 20: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 20: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 20: [----------] 18 tests from KernelSetupTest (4 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 18 tests from 1 test suite ran. (5 ms total) 20: [ PASSED ] 18 tests. 20/81 Test #20: NbnxmTests ..................................... Passed 0.04 sec test 21 Start 21: CommandLineUnitTests 21: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 21: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/commandline/tests 21: Test timeout computed to be: 30 21: [==========] Running 60 tests from 7 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from CommandLineHelpModuleTest 21: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 21: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (6 ms) 21: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 21: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 21: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 21: [ OK ] CommandLineHelpModuleTest.ExportsHelp (2 ms) 21: [----------] 3 tests from CommandLineHelpModuleTest (9 ms total) 21: 21: [----------] 7 tests from CommandLineHelpWriterTest 21: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 21: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (2 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 21: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 21: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 21: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 21: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 21: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 21: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 21: [----------] 7 tests from CommandLineHelpWriterTest (6 ms total) 21: 21: [----------] 6 tests from CommandLineModuleManagerTest 21: [ RUN ] CommandLineModuleManagerTest.RunsModule 21: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 21: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 21: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 21: 21: [----------] 13 tests from CommandLineParserTest 21: [ RUN ] CommandLineParserTest.HandlesSingleValues 21: [ OK ] CommandLineParserTest.HandlesSingleValues (3 ms) 21: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 21: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 21: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 21: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 21: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (2 ms) 21: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 21: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesString 21: [ OK ] CommandLineParserTest.HandlesString (0 ms) 21: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 21: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (6 ms) 21: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 21: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 21: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 21: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 21: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 21: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 21: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 21: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 21: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 21: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 21: [----------] 13 tests from CommandLineParserTest (12 ms total) 21: 21: [----------] 6 tests from CommandLineProgramContextTest 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 21: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 21: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 21: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 21: 21: [----------] 3 tests from OutputNamesTest 21: [ RUN ] OutputNamesTest.CanBeSuffixed 21: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 21: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 21: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 21: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 21: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 21: [----------] 3 tests from OutputNamesTest (0 ms total) 21: 21: [----------] 22 tests from ParseCommonArgsTest 21: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 21: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 21: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 21: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 21: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 21: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 21: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 21: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 21: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 21: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 21: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 21: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 21: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 21: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 21: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 21: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 21: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 21: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 21: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 21: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 21: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 21: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 21: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 21: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 21: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 21: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 21: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 21: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 21: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 21: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 21: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 21: [----------] 22 tests from ParseCommonArgsTest (2 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 60 tests from 7 test suites ran. (32 ms total) 21: [ PASSED ] 60 tests. 21/81 Test #21: CommandLineUnitTests ........................... Passed 0.06 sec test 22 Start 22: DomDecTests 22: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/DomDecTests.xml" 22: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests 22: Test timeout computed to be: 30 22: [==========] Running 9 tests from 2 test suites. 22: [----------] Global test environment set-up. 22: [----------] 7 tests from HashedMap 22: [ RUN ] HashedMap.InsertsFinds 22: [ OK ] HashedMap.InsertsFinds (0 ms) 22: [ RUN ] HashedMap.NegativeKeysWork 22: [ OK ] HashedMap.NegativeKeysWork (0 ms) 22: [ RUN ] HashedMap.InsertsErases 22: [ OK ] HashedMap.InsertsErases (0 ms) 22: [ RUN ] HashedMap.InsertsOrAssigns 22: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 22: [ RUN ] HashedMap.Clears 22: [ OK ] HashedMap.Clears (0 ms) 22: [ RUN ] HashedMap.LinkedEntries 22: [ OK ] HashedMap.LinkedEntries (0 ms) 22: [ RUN ] HashedMap.ResizesTable 22: [ OK ] HashedMap.ResizesTable (0 ms) 22: [----------] 7 tests from HashedMap (0 ms total) 22: 22: [----------] 2 tests from LocalAtomSetManager 22: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 22: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 22: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 22: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 22: [----------] 2 tests from LocalAtomSetManager (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 9 tests from 2 test suites ran. (0 ms total) 22: [ PASSED ] 9 tests. 22/81 Test #22: DomDecTests .................................... Passed 0.04 sec test 23 Start 23: DomDecMpiTests 23: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/DomDecMpiTests.xml" 23: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/domdec/tests 23: Test timeout computed to be: 30 23: [==========] Running 4 tests from 1 test suite. 23: [----------] Global test environment set-up. 23: [----------] 4 tests from HaloExchangeTest 23: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 23: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (50 ms) 23: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 23: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (37 ms) 23: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 23: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (22 ms) 23: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 23: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (31 ms) 23: [----------] 4 tests from HaloExchangeTest (142 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 4 tests from 1 test suite ran. (142 ms total) 23: [ PASSED ] 4 tests. 23/81 Test #23: DomDecMpiTests ................................. Passed 0.34 sec test 24 Start 24: EwaldUnitTests 24: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/EwaldUnitTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/ewald/tests 24: Test timeout computed to be: 30 24: [==========] Running 407 tests from 9 test suites. 24: [----------] Global test environment set-up. 24: [----------] 6 tests from SeparatePmeRanksPermittedTest 24: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 24: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 24: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (8 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 24: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 24: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 24: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 24: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 24: [----------] 6 tests from SeparatePmeRanksPermittedTest (8 ms total) 24: 24: [----------] 108 tests from Pme_SplineAndSpreadTest 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (338 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (10 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (10 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (5 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (7 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (5 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (6 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (16 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (6 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (7 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (4 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (7 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (11 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (12 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (9 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (9 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (15 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (10 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (4 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (8 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (9 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (26 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (6 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (5 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (5 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (23 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (23 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (5 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (5 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (4 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (29 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (13 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (9 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (12 ms) 24: [----------] 108 tests from Pme_SplineAndSpreadTest (838 ms total) 24: 24: [----------] 64 tests from Pme_SolveTest 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (8 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (7 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (6 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (7 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (2 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (6 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (4 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (9 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (5 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [----------] 64 tests from Pme_SolveTest (76 ms total) 24: 24: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (4 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (4 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (11 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (5 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (34 ms total) 24: 24: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (3 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (5 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (5 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (9 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (5 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (39 ms total) 24: 24: [----------] 64 tests from PmeDiffEps_SolveTest 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (12 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (9 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (7 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (8 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [----------] 64 tests from PmeDiffEps_SolveTest (60 ms total) 24: 24: [----------] 72 tests from Pme_GatherTest 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (2 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (4 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (6 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (7 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (3 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (8 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (8 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (7 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (8 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (6 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [----------] 72 tests from Pme_GatherTest (93 ms total) 24: 24: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (9 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (3 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 24: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (13 ms total) 24: 24: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (3 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (10 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (10 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (11 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (7 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (10 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (8 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (15 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (5 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (10 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (10 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (3 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (14 ms) 24: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (154 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 407 tests from 9 test suites ran. (1317 ms total) 24: [ PASSED ] 311 tests. 24: [ SKIPPED ] 96 tests, listed below: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24/81 Test #24: EwaldUnitTests ................................. Passed 1.54 sec test 25 Start 25: FFTUnitTests 25: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/FFTUnitTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fft/tests 25: Test timeout computed to be: 1920 25: [==========] Running 15 tests from 4 test suites. 25: [----------] Global test environment set-up. 25: [----------] 2 tests from ManyFFTTest 25: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 25: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (57 ms) 25: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 25: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (83 ms) 25: [----------] 2 tests from ManyFFTTest (141 ms total) 25: 25: [----------] 1 test from FFTTest 25: [ RUN ] FFTTest.Real2DLength18_15Test 25: [ OK ] FFTTest.Real2DLength18_15Test (17 ms) 25: [----------] 1 test from FFTTest (25 ms total) 25: 25: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (5 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (6 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (9 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (7 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (13 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (50 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (62 ms) 25: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (160 ms total) 25: 25: [----------] 2 tests from Works/ParameterizedFFTTest3D 25: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 25: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (1 ms) 25: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 25: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (6 ms) 25: [----------] 2 tests from Works/ParameterizedFFTTest3D (9 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 15 tests from 4 test suites ran. (337 ms total) 25: [ PASSED ] 15 tests. 25/81 Test #25: FFTUnitTests ................................... Passed 0.51 sec test 26 Start 26: GpuUtilsUnitTests 26: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gpu_utils/tests 26: Test timeout computed to be: 30 26: [==========] Running 64 tests from 22 test suites. 26: [----------] Global test environment set-up. 26: [----------] 2 tests from ClfftInitializer 26: [ RUN ] ClfftInitializer.SingleInitializationWorks 26: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 26: [ RUN ] ClfftInitializer.TwoInitializationsWork 26: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 26: [----------] 2 tests from ClfftInitializer (0 ms total) 26: 26: [----------] 1 test from DevicesAvailable 26: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 26: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 26: [----------] 1 test from DevicesAvailable (0 ms total) 26: 26: [----------] 1 test from DeviceStreamManagerTest 26: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 26: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 26: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 26: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 26: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 26: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 26: 26: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 26: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 26: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 26: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 26: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 26: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 26: 26: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 26: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 26: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 26: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 26: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 26: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 26: 26: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 26: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 26: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 26: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 26: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 26: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 26: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.Swap 26: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.Comparison 26: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 26: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 26: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.Swap 26: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.Comparison 26: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 26: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.Swap 26: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.Comparison 26: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 26: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 26: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.Swap 26: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.Comparison 26: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 26: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 26: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 26: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 26: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 26: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 26: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 26: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 26: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 26: 26: [----------] 1 test from HostAllocatorUntypedTest 26: [ RUN ] HostAllocatorUntypedTest.Comparison 26: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 26: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 26: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/0.Move 26: [ OK ] AllocatorTest/0.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/0 (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 26: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/1.Move 26: [ OK ] AllocatorTest/1.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/1 (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 26: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/2.Move 26: [ OK ] AllocatorTest/2.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/2 (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 26: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/3.Move 26: [ OK ] AllocatorTest/3.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/3 (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 64 tests from 22 test suites ran. (1 ms total) 26: [ PASSED ] 64 tests. 26/81 Test #26: GpuUtilsUnitTests .............................. Passed 0.24 sec test 27 Start 27: HardwareUnitTests 27: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/HardwareUnitTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/hardware/tests 27: Test timeout computed to be: 30 27: [==========] Running 21 tests from 9 test suites. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CpuInfoTest 27: [ RUN ] CpuInfoTest.SupportLevel 27: [ OK ] CpuInfoTest.SupportLevel (41 ms) 27: [----------] 1 test from CpuInfoTest (41 ms total) 27: 27: [----------] 4 tests from HardwareTopologyTest 27: [ RUN ] HardwareTopologyTest.Execute 27: [ OK ] HardwareTopologyTest.Execute (101 ms) 27: [ RUN ] HardwareTopologyTest.HwlocExecute 27: [ OK ] HardwareTopologyTest.HwlocExecute (95 ms) 27: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 27: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (113 ms) 27: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 27: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (99 ms) 27: [----------] 4 tests from HardwareTopologyTest (409 ms total) 27: 27: [----------] 1 test from DevicesManagerTest 27: [ RUN ] DevicesManagerTest.Serialization 27: [ OK ] DevicesManagerTest.Serialization (0 ms) 27: [----------] 1 test from DevicesManagerTest (0 ms total) 27: 27: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (34 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (12 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (4 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (7 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (7 ms) 27: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (67 ms total) 27: 27: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (23 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (7 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 27: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (34 ms total) 27: 27: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 27: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 27: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (29 ms) 27: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 27: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (7 ms) 27: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (37 ms total) 27: 27: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 27: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (40 ms) 27: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (40 ms total) 27: 27: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 27: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (231 ms) 27: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (231 ms total) 27: 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 27: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (106 ms) 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (106 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 21 tests from 9 test suites ran. (969 ms total) 27: [ PASSED ] 21 tests. 27/81 Test #27: HardwareUnitTests .............................. Passed 1.03 sec test 28 Start 28: MathUnitTests 28: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MathUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/math/tests 28: Test timeout computed to be: 30 28: [==========] Running 301 tests from 38 test suites. 28: [----------] Global test environment set-up. 28: [----------] 1 test from EmptyArrayRefWithPaddingTest 28: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 28: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 28: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 28: 28: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 28: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 28: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 28: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 28: 28: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 28: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 28: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 28: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 28: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 28: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 28: 28: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 28: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 28: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 28: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 28: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 28: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 28: 28: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 28: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 28: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 28: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 28: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 28: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 28: 28: [----------] 11 tests from TranslateAndScaleTest 28: [ RUN ] TranslateAndScaleTest.identityTransformation 28: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 28: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 28: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 28: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 28: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 28: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 28: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 28: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingIdentity 28: [ OK ] TranslateAndScaleTest.scalingIdentity (5 ms) 28: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 28: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 28: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 28: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 28: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 28: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 28: [----------] 11 tests from TranslateAndScaleTest (5 ms total) 28: 28: [----------] 3 tests from AffineTransformationTest 28: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 28: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (11 ms) 28: [ RUN ] AffineTransformationTest.applyTransformationToVectors 28: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 28: [ RUN ] AffineTransformationTest.retrieveGradient 28: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 28: [----------] 3 tests from AffineTransformationTest (11 ms total) 28: 28: [----------] 12 tests from DensitySimilarityTest 28: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 28: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 28: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 28: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (11 ms) 28: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 28: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 28: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 28: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 28: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 28: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 28: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 28: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (15 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 28: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (80 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (79 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (6 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 28: [----------] 12 tests from DensitySimilarityTest (194 ms total) 28: 28: [----------] 6 tests from StructureSimilarityTest 28: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 28: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (5 ms) 28: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 28: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 28: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 28: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 28: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 28: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 28: [----------] 6 tests from StructureSimilarityTest (5 ms total) 28: 28: [----------] 8 tests from ExponentialMovingAverage 28: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 28: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 28: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 28: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 28: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 28: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 28: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 28: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 28: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 28: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 28: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 28: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 28: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 28: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 28: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 28: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 28: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 28: 28: [----------] 21 tests from FunctionTest 28: [ RUN ] FunctionTest.StaticLog2 28: [ OK ] FunctionTest.StaticLog2 (3 ms) 28: [ RUN ] FunctionTest.Log2I32Bit 28: [ OK ] FunctionTest.Log2I32Bit (3 ms) 28: [ RUN ] FunctionTest.Log2I64Bit 28: [ OK ] FunctionTest.Log2I64Bit (0 ms) 28: [ RUN ] FunctionTest.GreatestCommonDivisor 28: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 28: [ RUN ] FunctionTest.InvsqrtFloat 28: [ OK ] FunctionTest.InvsqrtFloat (3 ms) 28: [ RUN ] FunctionTest.InvsqrtDouble 28: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 28: [ RUN ] FunctionTest.InvsqrtInteger 28: [ OK ] FunctionTest.InvsqrtInteger (3 ms) 28: [ RUN ] FunctionTest.InvcbrtFloat 28: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 28: [ RUN ] FunctionTest.InvcbrtDouble 28: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 28: [ RUN ] FunctionTest.InvcbrtInteger 28: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 28: [ RUN ] FunctionTest.SixthrootFloat 28: [ OK ] FunctionTest.SixthrootFloat (0 ms) 28: [ RUN ] FunctionTest.SixthrootDouble 28: [ OK ] FunctionTest.SixthrootDouble (0 ms) 28: [ RUN ] FunctionTest.SixthrootInteger 28: [ OK ] FunctionTest.SixthrootInteger (0 ms) 28: [ RUN ] FunctionTest.InvsixthrootFloat 28: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 28: [ RUN ] FunctionTest.InvsixthrootDouble 28: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 28: [ RUN ] FunctionTest.InvsixthrootInteger 28: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 28: [ RUN ] FunctionTest.Powers 28: [ OK ] FunctionTest.Powers (0 ms) 28: [ RUN ] FunctionTest.ErfInvFloat 28: [ OK ] FunctionTest.ErfInvFloat (0 ms) 28: [ RUN ] FunctionTest.ErfInvDouble 28: [ OK ] FunctionTest.ErfInvDouble (0 ms) 28: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 28: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 28: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 28: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 28: [----------] 21 tests from FunctionTest (17 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/0, where TypeParam = char 28: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/0 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 28: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/1 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/2, where TypeParam = int 28: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/2 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/3, where TypeParam = unsigned int 28: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/3 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/4, where TypeParam = long 28: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/4 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/5, where TypeParam = unsigned long 28: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/5 (0 ms total) 28: 28: [----------] 4 tests from GaussianOn1DLattice 28: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 28: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 28: [ RUN ] GaussianOn1DLattice.isCorrect 28: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 28: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 28: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 28: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 28: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 28: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 28: 28: [----------] 9 tests from GaussTransformTest 28: [ RUN ] GaussTransformTest.isZeroUponConstruction 28: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 28: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 28: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 28: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 28: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 28: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 28: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 28: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 28: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 28: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 28: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 28: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 28: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 28: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 28: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 28: [ RUN ] GaussTransformTest.view 28: [ OK ] GaussTransformTest.view (0 ms) 28: [----------] 9 tests from GaussTransformTest (0 ms total) 28: 28: [----------] 3 tests from DensityFittingForce 28: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 28: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 28: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 28: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 28: [ RUN ] DensityFittingForce.pullsTowardsDerivative 28: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 28: [----------] 3 tests from DensityFittingForce (0 ms total) 28: 28: [----------] 2 tests from InvertMatrixTest 28: [ RUN ] InvertMatrixTest.IdentityIsImpotent 28: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 28: [ RUN ] InvertMatrixTest.ComputesInverse 28: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 28: [----------] 2 tests from InvertMatrixTest (0 ms total) 28: 28: [----------] 2 tests from InvertBoxMatrixTest 28: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 28: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 28: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 28: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 28: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 28: 28: [----------] 17 tests from MatrixTest 28: [ RUN ] MatrixTest.canSetFromArray 28: [ OK ] MatrixTest.canSetFromArray (0 ms) 28: [ RUN ] MatrixTest.canSetStaticallyFromList 28: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 28: [ RUN ] MatrixTest.canConstructAndFill 28: [ OK ] MatrixTest.canConstructAndFill (0 ms) 28: [ RUN ] MatrixTest.canSetValues 28: [ OK ] MatrixTest.canSetValues (0 ms) 28: [ RUN ] MatrixTest.canCopyAssign 28: [ OK ] MatrixTest.canCopyAssign (0 ms) 28: [ RUN ] MatrixTest.canSwap 28: [ OK ] MatrixTest.canSwap (0 ms) 28: [ RUN ] MatrixTest.staticMultiDimArrayExtent 28: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 28: [ RUN ] MatrixTest.determinantWorks 28: [ OK ] MatrixTest.determinantWorks (0 ms) 28: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 28: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 28: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 28: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 28: [ RUN ] MatrixTest.traceWorks 28: [ OK ] MatrixTest.traceWorks (0 ms) 28: [ RUN ] MatrixTest.transposeWorks 28: [ OK ] MatrixTest.transposeWorks (0 ms) 28: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 28: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 28: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 28: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 28: [ RUN ] MatrixTest.canFillLegacyMatrix 28: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 28: [ RUN ] MatrixTest.IdentityMatrix 28: [ OK ] MatrixTest.IdentityMatrix (0 ms) 28: [ RUN ] MatrixTest.MatrixVectorMultiplication 28: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 28: [----------] 17 tests from MatrixTest (0 ms total) 28: 28: [----------] 25 tests from MultiDimArrayTest 28: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 28: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 28: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 28: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 28: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 28: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 28: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 28: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 28: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 28: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 28: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 28: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 28: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSwapStatic 28: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSwapDynamic 28: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 28: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 28: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 28: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 28: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 28: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 28: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 28: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 28: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 28: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 28: [ RUN ] MultiDimArrayTest.conversionToView 28: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 28: [ RUN ] MultiDimArrayTest.conversionToConstView 28: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 28: [ RUN ] MultiDimArrayTest.viewBegin 28: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 28: [ RUN ] MultiDimArrayTest.viewEnd 28: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 28: [ RUN ] MultiDimArrayTest.constViewConstBegin 28: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 28: [ RUN ] MultiDimArrayTest.constViewConstEnd 28: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 28: [----------] 25 tests from MultiDimArrayTest (0 ms total) 28: 28: [----------] 4 tests from MultiDimArrayToMdSpanTest 28: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 28: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 28: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 28: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 28: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 28: 28: [----------] 9 tests from NelderMeadSimplexTest 28: [ RUN ] NelderMeadSimplexTest.BestVertex 28: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 28: [ RUN ] NelderMeadSimplexTest.WorstVertex 28: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 28: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 28: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 28: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 28: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 28: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 28: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 28: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 28: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 28: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 28: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 28: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 28: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 28: [ RUN ] NelderMeadSimplexTest.OrientedLength 28: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 28: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 28: 28: [----------] 2 tests from NelderMead 28: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 28: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 28: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 28: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 28: [----------] 2 tests from NelderMead (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 28: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ResizeWorks 28: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ReserveWorks 28: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/0.CanCopyAssign 28: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/0.CanMoveAssign 28: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/0.CanSwap 28: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 28: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ResizeWorks 28: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ReserveWorks 28: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/1.CanCopyAssign 28: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/1.CanMoveAssign 28: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/1.CanSwap 28: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 28: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ResizeWorks 28: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ReserveWorks 28: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/2.CanCopyAssign 28: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/2.CanMoveAssign 28: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/2.CanSwap 28: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 28: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ResizeWorks 28: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ReserveWorks 28: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/3.CanCopyAssign 28: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/3.CanMoveAssign 28: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/3.CanSwap 28: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 28: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ResizeWorks 28: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ReserveWorks 28: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/4.CanCopyAssign 28: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/4.CanMoveAssign 28: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/4.CanSwap 28: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 28: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ResizeWorks 28: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ReserveWorks 28: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/5.CanCopyAssign 28: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/5.CanMoveAssign 28: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/5.CanSwap 28: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 28: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ResizeWorks 28: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ReserveWorks 28: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/6.CanCopyAssign 28: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/6.CanMoveAssign 28: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/6.CanSwap 28: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 28: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ResizeWorks 28: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ReserveWorks 28: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/7.CanCopyAssign 28: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/7.CanMoveAssign 28: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/7.CanSwap 28: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 28: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ResizeWorks 28: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ReserveWorks 28: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/8.CanCopyAssign 28: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/8.CanMoveAssign 28: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/8.CanSwap 28: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 28: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ResizeWorks 28: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ReserveWorks 28: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/9.CanCopyAssign 28: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/9.CanMoveAssign 28: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/9.CanSwap 28: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 28: 28: [----------] 39 tests from RVecTest 28: [ RUN ] RVecTest.CanBeStoredInVector 28: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 28: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 28: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 28: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 28: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 28: [ RUN ] RVecTest.WorksAsMutable_rvec 28: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 28: [ RUN ] RVecTest.WorksAs_rvec_Array 28: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 28: [ RUN ] RVecTest.ComparesEqual 28: [ OK ] RVecTest.ComparesEqual (0 ms) 28: [ RUN ] RVecTest.ComparesUnequal 28: [ OK ] RVecTest.ComparesUnequal (0 ms) 28: [ RUN ] RVecTest.CanAddRVecToRvec 28: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 28: [ RUN ] RVecTest.CanAddAssignRVecToRvec 28: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 28: [ RUN ] RVecTest.CanSubtractRVecFromRvec 28: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 28: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 28: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 28: [ RUN ] RVecTest.CanDotProductRVecByRvec 28: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 28: [ RUN ] RVecTest.CanCrossProductRVecByRvec 28: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 28: [ RUN ] RVecTest.CanDivideRVecInplace 28: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 28: [ RUN ] RVecTest.CanScaleRVec 28: [ OK ] RVecTest.CanScaleRVec (0 ms) 28: [ RUN ] RVecTest.CanDivideRVec 28: [ OK ] RVecTest.CanDivideRVec (0 ms) 28: [ RUN ] RVecTest.CanDoUnitvFromRVec 28: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 28: [ RUN ] RVecTest.CanSqLengthOfRVec 28: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanLengthOfRVec 28: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanCastToRVec 28: [ OK ] RVecTest.CanCastToRVec (0 ms) 28: [ RUN ] RVecTest.CanCastToDVec 28: [ OK ] RVecTest.CanCastToDVec (0 ms) 28: [ RUN ] RVecTest.CanLeftScalarMultiply 28: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 28: [ RUN ] RVecTest.CanRightScalarMultiply 28: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 28: [ RUN ] RVecTest.CanGetUnitvFromRVec 28: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 28: [ RUN ] RVecTest.CanGetSqLengthOfRVec 28: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanGetLengthOfRVec 28: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanDoCrossProductOfRVec 28: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 28: [ RUN ] RVecTest.CanDoDotProductOfRVec 28: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 28: [ RUN ] RVecTest.CanScaleByVector 28: [ OK ] RVecTest.CanScaleByVector (0 ms) 28: [ RUN ] RVecTest.asIVec 28: [ OK ] RVecTest.asIVec (0 ms) 28: [ RUN ] RVecTest.elementWiseMin 28: [ OK ] RVecTest.elementWiseMin (0 ms) 28: [ RUN ] RVecTest.elementWiseMax 28: [ OK ] RVecTest.elementWiseMax (0 ms) 28: [ RUN ] RVecTest.WorksAs_dvec_Reference 28: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 28: [ RUN ] RVecTest.WorksAs_ivec_Reference 28: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 28: [ RUN ] RVecTest.WorksAs_rvec_Reference 28: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 28: [ RUN ] RVecTest.CopyConstructorWorks 28: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 28: [ RUN ] RVecTest.CopyAssignmentWorks 28: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 28: [ RUN ] RVecTest.MoveConstructorWorks 28: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 28: [ RUN ] RVecTest.MoveAssignmentWorks 28: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 28: [----------] 39 tests from RVecTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 301 tests from 38 test suites ran. (239 ms total) 28: [ PASSED ] 301 tests. 28/81 Test #28: MathUnitTests .................................. Passed 0.32 sec test 29 Start 29: MdrunUtilityUnitTests 29: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests 29: Test timeout computed to be: 30 29: [==========] Running 17 tests from 1 test suite. 29: [----------] Global test environment set-up. 29: [----------] 17 tests from ThreadAffinityTest 29: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 29: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 29: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (7 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 29: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 29: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 29: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 29: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 29: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 29: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 29: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 29: NOTE: Affinity setting failed. 29: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 29: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (17 ms) 29: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 29: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 29: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 29: NOTE: Affinity setting for 1/2 threads failed. 29: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 29: [----------] 17 tests from ThreadAffinityTest (28 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 17 tests from 1 test suite ran. (28 ms total) 29: [ PASSED ] 17 tests. 29/81 Test #29: MdrunUtilityUnitTests .......................... Passed 0.09 sec test 30 Start 30: MdrunUtilityMpiUnitTests 30: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdrunutility/tests 30: Test timeout computed to be: 30 30: [==========] Running 13 tests from 2 test suites. 30: [----------] Global test environment set-up. 30: [----------] 6 tests from ThreadAffinityMultiRankTest 30: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 30: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (59 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 30: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (135 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 30: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (88 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 30: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (47 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 30: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (55 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 30: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (139 ms) 30: [----------] 6 tests from ThreadAffinityMultiRankTest (527 ms total) 30: 30: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (135 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (51 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (83 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (87 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (99 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (88 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (67 ms) 30: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (615 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 13 tests from 2 test suites ran. (1143 ms total) 30: [ PASSED ] 13 tests. 30/81 Test #30: MdrunUtilityMpiUnitTests ....................... Passed 1.20 sec test 31 Start 31: MDSpanTests 31: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MDSpanTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdspan/tests 31: Test timeout computed to be: 30 31: [==========] Running 32 tests from 7 test suites. 31: [----------] Global test environment set-up. 31: [----------] 4 tests from BasicAccessorPolicy 31: [ RUN ] BasicAccessorPolicy.Decay 31: [ OK ] BasicAccessorPolicy.Decay (0 ms) 31: [ RUN ] BasicAccessorPolicy.Access 31: [ OK ] BasicAccessorPolicy.Access (0 ms) 31: [ RUN ] BasicAccessorPolicy.Offset 31: [ OK ] BasicAccessorPolicy.Offset (0 ms) 31: [ RUN ] BasicAccessorPolicy.CopyAccessor 31: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 31: [----------] 4 tests from BasicAccessorPolicy (8 ms total) 31: 31: [----------] 4 tests from ExtentsTest 31: [ RUN ] ExtentsTest.Construction 31: [ OK ] ExtentsTest.Construction (0 ms) 31: [ RUN ] ExtentsTest.PurelyStatic 31: [ OK ] ExtentsTest.PurelyStatic (0 ms) 31: [ RUN ] ExtentsTest.RankNought 31: [ OK ] ExtentsTest.RankNought (0 ms) 31: [ RUN ] ExtentsTest.Assignment 31: [ OK ] ExtentsTest.Assignment (0 ms) 31: [----------] 4 tests from ExtentsTest (0 ms total) 31: 31: [----------] 8 tests from MdSpanExtension 31: [ RUN ] MdSpanExtension.SlicingAllStatic 31: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 31: [ RUN ] MdSpanExtension.SlicingDynamic 31: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 31: [ RUN ] MdSpanExtension.SlicingAllStatic3D 31: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 31: [ RUN ] MdSpanExtension.SlicingEqualsView3D 31: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 31: [ RUN ] MdSpanExtension.additionWorks 31: [ OK ] MdSpanExtension.additionWorks (0 ms) 31: [ RUN ] MdSpanExtension.subtractionWorks 31: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 31: [ RUN ] MdSpanExtension.multiplicationWorks 31: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 31: [ RUN ] MdSpanExtension.divisionWorks 31: [ OK ] MdSpanExtension.divisionWorks (0 ms) 31: [----------] 8 tests from MdSpanExtension (0 ms total) 31: 31: [----------] 3 tests from LayoutTests 31: [ RUN ] LayoutTests.LayoutRightConstruction 31: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 31: [ RUN ] LayoutTests.LayoutRightProperties 31: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 31: [ RUN ] LayoutTests.LayoutRightOperator 31: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 31: [----------] 3 tests from LayoutTests (0 ms total) 31: 31: [----------] 1 test from MdSpanTest 31: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 31: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 31: [----------] 1 test from MdSpanTest (0 ms total) 31: 31: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 31: [ RUN ] MdSpanTest/0.Rank 31: [ OK ] MdSpanTest/0.Rank (0 ms) 31: [ RUN ] MdSpanTest/0.DynamicRank 31: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 31: [ RUN ] MdSpanTest/0.Extents 31: [ OK ] MdSpanTest/0.Extents (0 ms) 31: [ RUN ] MdSpanTest/0.Strides 31: [ OK ] MdSpanTest/0.Strides (0 ms) 31: [ RUN ] MdSpanTest/0.Properties 31: [ OK ] MdSpanTest/0.Properties (0 ms) 31: [ RUN ] MdSpanTest/0.Operator 31: [ OK ] MdSpanTest/0.Operator (0 ms) 31: [----------] 6 tests from MdSpanTest/0 (0 ms total) 31: 31: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 31: [ RUN ] MdSpanTest/1.Rank 31: [ OK ] MdSpanTest/1.Rank (0 ms) 31: [ RUN ] MdSpanTest/1.DynamicRank 31: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 31: [ RUN ] MdSpanTest/1.Extents 31: [ OK ] MdSpanTest/1.Extents (0 ms) 31: [ RUN ] MdSpanTest/1.Strides 31: [ OK ] MdSpanTest/1.Strides (0 ms) 31: [ RUN ] MdSpanTest/1.Properties 31: [ OK ] MdSpanTest/1.Properties (0 ms) 31: [ RUN ] MdSpanTest/1.Operator 31: [ OK ] MdSpanTest/1.Operator (0 ms) 31: [----------] 6 tests from MdSpanTest/1 (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 32 tests from 7 test suites ran. (8 ms total) 31: [ PASSED ] 32 tests. 31/81 Test #31: MDSpanTests .................................... Passed 0.06 sec test 32 Start 32: MdtypesUnitTest 32: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdtypesUnitTest.xml" 32: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/mdtypes/tests 32: Test timeout computed to be: 30 32: [==========] Running 93 tests from 6 test suites. 32: [----------] Global test environment set-up. 32: [----------] 4 tests from ObservablesReducerTest 32: [ RUN ] ObservablesReducerTest.CanMoveAssign 32: [ OK ] ObservablesReducerTest.CanMoveAssign (15 ms) 32: [ RUN ] ObservablesReducerTest.CanMoveConstruct 32: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 32: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 32: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 32: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 32: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 32: [----------] 4 tests from ObservablesReducerTest (15 ms total) 32: 32: [----------] 2 tests from CheckpointDataTest 32: [ RUN ] CheckpointDataTest.SingleDataTest 32: [ OK ] CheckpointDataTest.SingleDataTest (5 ms) 32: [ RUN ] CheckpointDataTest.MultiDataTest 32: [ OK ] CheckpointDataTest.MultiDataTest (16 ms) 32: [----------] 2 tests from CheckpointDataTest (21 ms total) 32: 32: [----------] 7 tests from ForceBuffers 32: [ RUN ] ForceBuffers.ConstructsUnpinned 32: [ OK ] ForceBuffers.ConstructsUnpinned (6 ms) 32: [ RUN ] ForceBuffers.ConstructsPinned 32: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 32: [ RUN ] ForceBuffers.ConstructsEmpty 32: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 32: [ RUN ] ForceBuffers.ResizeWorks 32: [ OK ] ForceBuffers.ResizeWorks (0 ms) 32: [ RUN ] ForceBuffers.PaddingWorks 32: [ OK ] ForceBuffers.PaddingWorks (0 ms) 32: [ RUN ] ForceBuffers.CopyWorks 32: [ OK ] ForceBuffers.CopyWorks (0 ms) 32: [ RUN ] ForceBuffers.CopyDoesNotPin 32: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 32: [----------] 7 tests from ForceBuffers (6 ms total) 32: 32: [----------] 5 tests from MultipleTimeStepping 32: [ RUN ] MultipleTimeStepping.ChecksNumLevels 32: [ OK ] MultipleTimeStepping.ChecksNumLevels (7 ms) 32: [ RUN ] MultipleTimeStepping.SelectsForceGroups 32: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 32: [ RUN ] MultipleTimeStepping.ChecksStepFactor 32: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 32: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 32: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (3 ms) 32: [ RUN ] MultipleTimeStepping.ChecksIntegrator 32: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 32: [----------] 5 tests from MultipleTimeStepping (11 ms total) 32: 32: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 32: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (3 ms total) 32: 32: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 32: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 93 tests from 6 test suites ran. (58 ms total) 32: [ PASSED ] 93 tests. 32/81 Test #32: MdtypesUnitTest ................................ Passed 0.13 sec test 33 Start 33: OnlineHelpUnitTests 33: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/onlinehelp/tests 33: Test timeout computed to be: 30 33: [==========] Running 22 tests from 4 test suites. 33: [----------] Global test environment set-up. 33: [----------] 6 tests from TextTableFormatterTest 33: [ RUN ] TextTableFormatterTest.HandlesBasicCase 33: [ OK ] TextTableFormatterTest.HandlesBasicCase (4 ms) 33: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 33: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (3 ms) 33: [ RUN ] TextTableFormatterTest.HandlesIndentation 33: [ OK ] TextTableFormatterTest.HandlesIndentation (3 ms) 33: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 33: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (4 ms) 33: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 33: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (3 ms) 33: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 33: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (3 ms) 33: [----------] 6 tests from TextTableFormatterTest (24 ms total) 33: 33: [----------] 3 tests from HelpManagerTest 33: [ RUN ] HelpManagerTest.HandlesRootTopic 33: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 33: [ RUN ] HelpManagerTest.HandlesSubTopics 33: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 33: [ RUN ] HelpManagerTest.HandlesInvalidTopics 33: [ OK ] HelpManagerTest.HandlesInvalidTopics (11 ms) 33: [----------] 3 tests from HelpManagerTest (12 ms total) 33: 33: [----------] 2 tests from HelpTopicFormattingTest 33: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 33: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (3 ms) 33: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 33: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 33: [----------] 2 tests from HelpTopicFormattingTest (4 ms total) 33: 33: [----------] 11 tests from HelpWriterContextTest 33: [ RUN ] HelpWriterContextTest.FormatsParagraphs 33: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 33: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 33: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 33: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsLiteralText 33: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 33: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 33: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsBulletList 33: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 33: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 33: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsGridTable 33: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsTitles 33: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 33: [----------] 11 tests from HelpWriterContextTest (1 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 22 tests from 4 test suites ran. (41 ms total) 33: [ PASSED ] 22 tests. 33/81 Test #33: OnlineHelpUnitTests ............................ Passed 0.10 sec test 34 Start 34: OptionsUnitTests 34: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/OptionsUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/options/tests 34: Test timeout computed to be: 30 34: [==========] Running 111 tests from 18 test suites. 34: [----------] Global test environment set-up. 34: [----------] 5 tests from AbstractOptionStorageTest 34: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 34: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 34: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 34: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 34: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 34: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 34: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 34: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 34: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 34: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 34: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 34: 34: [----------] 10 tests from FileNameOptionTest 34: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 34: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 34: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 34: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 34: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 34: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 34: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 34: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 34: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 34: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 34: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 34: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 34: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 34: [----------] 10 tests from FileNameOptionTest (0 ms total) 34: 34: [----------] 15 tests from FileNameOptionManagerTest 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 34: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 34: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 34: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 34: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 34: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 34: [----------] 15 tests from FileNameOptionManagerTest (0 ms total) 34: 34: [----------] 1 test from OptionsTest 34: [ RUN ] OptionsTest.FailsOnNonsafeStorage 34: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 34: [----------] 1 test from OptionsTest (0 ms total) 34: 34: [----------] 9 tests from OptionsAssignerTest 34: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 34: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 34: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 34: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 34: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesMissingValue 34: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesExtraValue 34: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesGroups 34: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesSections 34: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 34: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 34: [----------] 9 tests from OptionsAssignerTest (0 ms total) 34: 34: [----------] 4 tests from OptionsAssignerBooleanTest 34: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 34: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 34: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 34: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 34: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 34: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 34: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 34: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 34: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 34: 34: [----------] 13 tests from OptionsAssignerIntegerTest 34: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 34: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 34: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 34: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 34: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 34: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 34: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 34: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 34: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 34: 34: [----------] 5 tests from OptionsAssignerDoubleTest 34: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 34: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 34: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 34: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 34: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (8 ms) 34: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 34: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 34: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 34: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 34: [----------] 5 tests from OptionsAssignerDoubleTest (8 ms total) 34: 34: [----------] 9 tests from OptionsAssignerStringTest 34: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 34: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 34: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 34: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 34: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 34: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 34: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 34: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 34: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 34: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 34: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 34: 34: [----------] 6 tests from OptionsAssignerEnumTest 34: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 34: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 34: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 34: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 34: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 34: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 34: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 34: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 34: 34: [----------] 8 tests from RepeatingOptionSectionTest 34: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 34: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 34: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 34: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 34: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 34: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 34: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 34: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 34: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 34: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 34: 34: [----------] 1 test from TimeUnitManagerTest 34: [ RUN ] TimeUnitManagerTest.BasicOperations 34: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 34: [----------] 1 test from TimeUnitManagerTest (0 ms total) 34: 34: [----------] 4 tests from TimeUnitBehaviorTest 34: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 34: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 34: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 34: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 34: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 34: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 34: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 34: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 34: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 34: 34: [----------] 2 tests from TreeValueSupportAssignTest 34: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 34: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 34: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 34: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 34: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 34: 34: [----------] 1 test from TreeValueSupportAssignErrorTest 34: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 34: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 34: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 34: 34: [----------] 5 tests from TreeValueSupportCheckTest 34: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 34: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 34: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 34: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 34: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 34: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 34: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 34: 34: [----------] 6 tests from TreeValueSupportAdjustTest 34: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 34: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (6 ms) 34: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 34: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 34: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 34: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 34: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 34: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 34: [----------] 6 tests from TreeValueSupportAdjustTest (7 ms total) 34: 34: [----------] 7 tests from TreeValueSupportTest 34: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 34: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 34: [ OK ] TreeValueSupportTest.SupportsIntegerOption (6 ms) 34: [ RUN ] TreeValueSupportTest.SupportsInt64Option 34: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsStringOption 34: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsFloatOption 34: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 34: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsEnumOption 34: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 34: [----------] 7 tests from TreeValueSupportTest (8 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 111 tests from 18 test suites ran. (28 ms total) 34: [ PASSED ] 111 tests. 34/81 Test #34: OptionsUnitTests ............................... Passed 0.08 sec test 35 Start 35: PbcutilUnitTest 35: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 35: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pbcutil/tests 35: Test timeout computed to be: 30 35: [==========] Running 33 tests from 5 test suites. 35: [----------] Global test environment set-up. 35: [----------] 1 test from ShiftTest 35: [ RUN ] ShiftTest.CoordinateShiftWorks 35: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 35: [----------] 1 test from ShiftTest (0 ms total) 35: 35: [----------] 2 tests from MShift 35: [ RUN ] MShift.shiftsAndUnshifts 35: [ OK ] MShift.shiftsAndUnshifts (0 ms) 35: [ RUN ] MShift.shiftsAndUnshiftsSelf 35: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 35: [----------] 2 tests from MShift (0 ms total) 35: 35: [----------] 1 test from PbcTest 35: [ RUN ] PbcTest.CalcShiftsWorks 35: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 35: [----------] 1 test from PbcTest (0 ms total) 35: 35: [----------] 2 tests from PbcEnumsTest 35: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 35: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 35: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 35: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 35: [----------] 2 tests from PbcEnumsTest (0 ms total) 35: 35: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (17 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (6 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (2 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 35: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (33 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 33 tests from 5 test suites ran. (34 ms total) 35: [ PASSED ] 33 tests. 35/81 Test #35: PbcutilUnitTest ................................ Passed 0.10 sec test 36 Start 36: RandomUnitTests 36: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/RandomUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/random/tests 36: Test timeout computed to be: 30 36: [==========] Running 44 tests from 10 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from ExponentialDistributionTest 36: [ RUN ] ExponentialDistributionTest.Output 36: [ OK ] ExponentialDistributionTest.Output (3 ms) 36: [ RUN ] ExponentialDistributionTest.Logical 36: [ OK ] ExponentialDistributionTest.Logical (0 ms) 36: [ RUN ] ExponentialDistributionTest.Reset 36: [ OK ] ExponentialDistributionTest.Reset (0 ms) 36: [ RUN ] ExponentialDistributionTest.AltParam 36: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from ExponentialDistributionTest (4 ms total) 36: 36: [----------] 4 tests from GammaDistributionTest 36: [ RUN ] GammaDistributionTest.Output 36: [ OK ] GammaDistributionTest.Output (0 ms) 36: [ RUN ] GammaDistributionTest.Logical 36: [ OK ] GammaDistributionTest.Logical (0 ms) 36: [ RUN ] GammaDistributionTest.Reset 36: [ OK ] GammaDistributionTest.Reset (0 ms) 36: [ RUN ] GammaDistributionTest.AltParam 36: [ OK ] GammaDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from GammaDistributionTest (0 ms total) 36: 36: [----------] 4 tests from NormalDistributionTest 36: [ RUN ] NormalDistributionTest.Output 36: [ OK ] NormalDistributionTest.Output (3 ms) 36: [ RUN ] NormalDistributionTest.Logical 36: [ OK ] NormalDistributionTest.Logical (0 ms) 36: [ RUN ] NormalDistributionTest.Reset 36: [ OK ] NormalDistributionTest.Reset (0 ms) 36: [ RUN ] NormalDistributionTest.AltParam 36: [ OK ] NormalDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from NormalDistributionTest (3 ms total) 36: 36: [----------] 1 test from SeedTest 36: [ RUN ] SeedTest.makeRandomSeed 36: [ OK ] SeedTest.makeRandomSeed (0 ms) 36: [----------] 1 test from SeedTest (0 ms total) 36: 36: [----------] 6 tests from TabulatedNormalDistributionTest 36: [ RUN ] TabulatedNormalDistributionTest.Output14 36: [ OK ] TabulatedNormalDistributionTest.Output14 (3 ms) 36: [ RUN ] TabulatedNormalDistributionTest.Output16 36: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 36: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (3 ms) 36: [ RUN ] TabulatedNormalDistributionTest.Logical 36: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.Reset 36: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.AltParam 36: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 36: [----------] 6 tests from TabulatedNormalDistributionTest (7 ms total) 36: 36: [----------] 1 test from TabulatedNormalDistributionTableTest 36: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 36: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (1 ms) 36: [----------] 1 test from TabulatedNormalDistributionTableTest (1 ms total) 36: 36: [----------] 6 tests from ThreeFry2x64Test 36: [ RUN ] ThreeFry2x64Test.Logical 36: [ OK ] ThreeFry2x64Test.Logical (0 ms) 36: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 36: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 36: [ RUN ] ThreeFry2x64Test.Reseed 36: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 36: [ RUN ] ThreeFry2x64Test.Discard 36: [ OK ] ThreeFry2x64Test.Discard (0 ms) 36: [ RUN ] ThreeFry2x64Test.InvalidCounter 36: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 36: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 36: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 36: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 36: 36: [----------] 4 tests from UniformIntDistributionTest 36: [ RUN ] UniformIntDistributionTest.Output 36: [ OK ] UniformIntDistributionTest.Output (0 ms) 36: [ RUN ] UniformIntDistributionTest.Logical 36: [ OK ] UniformIntDistributionTest.Logical (0 ms) 36: [ RUN ] UniformIntDistributionTest.Reset 36: [ OK ] UniformIntDistributionTest.Reset (0 ms) 36: [ RUN ] UniformIntDistributionTest.AltParam 36: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 36: 36: [----------] 5 tests from UniformRealDistributionTest 36: [ RUN ] UniformRealDistributionTest.GenerateCanonical 36: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 36: [ RUN ] UniformRealDistributionTest.Output 36: [ OK ] UniformRealDistributionTest.Output (0 ms) 36: [ RUN ] UniformRealDistributionTest.Logical 36: [ OK ] UniformRealDistributionTest.Logical (0 ms) 36: [ RUN ] UniformRealDistributionTest.Reset 36: [ OK ] UniformRealDistributionTest.Reset (0 ms) 36: [ RUN ] UniformRealDistributionTest.AltParam 36: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 36: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 36: 36: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (5 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 36: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (6 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 44 tests from 10 test suites ran. (24 ms total) 36: [ PASSED ] 44 tests. 36/81 Test #36: RandomUnitTests ................................ Passed 0.09 sec test 37 Start 37: RestraintTests 37: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/RestraintTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/restraint/tests 37: Test timeout computed to be: 30 37: [==========] Running 1 test from 1 test suite. 37: [----------] Global test environment set-up. 37: [----------] 1 test from RestraintManager 37: [ RUN ] RestraintManager.restraintList 37: [ OK ] RestraintManager.restraintList (0 ms) 37: [----------] 1 test from RestraintManager (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 1 test from 1 test suite ran. (0 ms total) 37: [ PASSED ] 1 test. 37/81 Test #37: RestraintTests ................................. Passed 0.06 sec test 38 Start 38: TableUnitTests 38: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/TableUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tables/tests 38: Test timeout computed to be: 30 38: [==========] Running 20 tests from 2 test suites. 38: [----------] Global test environment set-up. 38: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 38: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 38: [ OK ] SplineTableTest/0.HandlesIncorrectInput (37 ms) 38: [ RUN ] SplineTableTest/0.Sinc 38: [ OK ] SplineTableTest/0.Sinc (0 ms) 38: [ RUN ] SplineTableTest/0.LJ12 38: [ OK ] SplineTableTest/0.LJ12 (32 ms) 38: [ RUN ] SplineTableTest/0.PmeCorrection 38: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 38: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 38: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (5 ms) 38: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 38: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (1 ms) 38: [ RUN ] SplineTableTest/0.TwoFunctions 38: [ OK ] SplineTableTest/0.TwoFunctions (61 ms) 38: [ RUN ] SplineTableTest/0.ThreeFunctions 38: [ OK ] SplineTableTest/0.ThreeFunctions (71 ms) 38: [ RUN ] SplineTableTest/0.Simd 38: [ OK ] SplineTableTest/0.Simd (10 ms) 38: [ RUN ] SplineTableTest/0.SimdTwoFunctions 38: [ OK ] SplineTableTest/0.SimdTwoFunctions (56 ms) 38: [----------] 10 tests from SplineTableTest/0 (279 ms total) 38: 38: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 38: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 38: [ OK ] SplineTableTest/1.HandlesIncorrectInput (2 ms) 38: [ RUN ] SplineTableTest/1.Sinc 38: [ OK ] SplineTableTest/1.Sinc (0 ms) 38: [ RUN ] SplineTableTest/1.LJ12 38: [ OK ] SplineTableTest/1.LJ12 (10 ms) 38: [ RUN ] SplineTableTest/1.PmeCorrection 38: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 38: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 38: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 38: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 38: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 38: [ RUN ] SplineTableTest/1.TwoFunctions 38: [ OK ] SplineTableTest/1.TwoFunctions (4 ms) 38: [ RUN ] SplineTableTest/1.ThreeFunctions 38: [ OK ] SplineTableTest/1.ThreeFunctions (4 ms) 38: [ RUN ] SplineTableTest/1.Simd 38: [ OK ] SplineTableTest/1.Simd (1 ms) 38: [ RUN ] SplineTableTest/1.SimdTwoFunctions 38: [ OK ] SplineTableTest/1.SimdTwoFunctions (4 ms) 38: [----------] 10 tests from SplineTableTest/1 (32 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 20 tests from 2 test suites ran. (312 ms total) 38: [ PASSED ] 20 tests. 38/81 Test #38: TableUnitTests ................................. Passed 0.36 sec test 39 Start 39: TaskAssignmentUnitTests 39: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/taskassignment/tests 39: Test timeout computed to be: 30 39: [==========] Running 3 tests from 2 test suites. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 39: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 39: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 39: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 39: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 39: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 39: 39: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 39: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 39: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (2 ms) 39: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (2 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 3 tests from 2 test suites ran. (2 ms total) 39: [ PASSED ] 3 tests. 39/81 Test #39: TaskAssignmentUnitTests ........................ Passed 0.02 sec test 40 Start 40: GmxTimingTests 40: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/GmxTimingTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/timing/tests 40: Test timeout computed to be: 30 40: [==========] Running 6 tests from 1 test suite. 40: [----------] Global test environment set-up. 40: [----------] 6 tests from TimingTest 40: [ RUN ] TimingTest.ElementCountingWorks 40: [ OK ] TimingTest.ElementCountingWorks (0 ms) 40: [ RUN ] TimingTest.ElementNoCountingWorks 40: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 40: [ RUN ] TimingTest.SubElementCountingWorks 40: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 40: [ RUN ] TimingTest.SubElementNoCountingWorks 40: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 40: [ RUN ] TimingTest.RunWallCycle 40: [ OK ] TimingTest.RunWallCycle (8 ms) 40: [ RUN ] TimingTest.RunWallCycleSub 40: [ OK ] TimingTest.RunWallCycleSub (0 ms) 40: [----------] 6 tests from TimingTest (8 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 6 tests from 1 test suite ran. (9 ms total) 40: [ PASSED ] 6 tests. 40/81 Test #40: GmxTimingTests ................................. Passed 0.06 sec test 41 Start 41: TopologyTest 41: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/TopologyTest.xml" 41: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/topology/tests 41: Test timeout computed to be: 30 41: [==========] Running 40 tests from 7 test suites. 41: [----------] Global test environment set-up. 41: [----------] 3 tests from ExclusionBlockTest 41: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 41: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 41: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 41: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 41: [ RUN ] ExclusionBlockTest.MergeExclusions 41: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 41: [----------] 3 tests from ExclusionBlockTest (0 ms total) 41: 41: [----------] 6 tests from InteractionListTest 41: [ RUN ] InteractionListTest.EmptyWorks 41: [ OK ] InteractionListTest.EmptyWorks (0 ms) 41: [ RUN ] InteractionListTest.CanAddInteractionArray 41: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 41: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 41: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 41: [ RUN ] InteractionListTest.CanAddInteractionPointer 41: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 41: [ RUN ] InteractionListTest.CanAddListToOtherList 41: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 41: [ RUN ] InteractionListTest.ClearingWorks 41: [ OK ] InteractionListTest.ClearingWorks (0 ms) 41: [----------] 6 tests from InteractionListTest (0 ms total) 41: 41: [----------] 5 tests from MtopTest 41: [ RUN ] MtopTest.RangeBasedLoop 41: [ OK ] MtopTest.RangeBasedLoop (0 ms) 41: [ RUN ] MtopTest.Operators 41: [ OK ] MtopTest.Operators (0 ms) 41: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 41: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 41: [ RUN ] MtopTest.AtomHasPerturbedChargeIn14Interaction 41: [ OK ] MtopTest.AtomHasPerturbedChargeIn14Interaction (0 ms) 41: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 41: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 41: [----------] 5 tests from MtopTest (0 ms total) 41: 41: [----------] 2 tests from IListRangeTest 41: [ RUN ] IListRangeTest.RangeBasedLoopWorks 41: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 41: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 41: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 41: [----------] 2 tests from IListRangeTest (0 ms total) 41: 41: [----------] 13 tests from StringTableTest 41: [ RUN ] StringTableTest.AddSingleEntry 41: [ OK ] StringTableTest.AddSingleEntry (8 ms) 41: [ RUN ] StringTableTest.CanAccessWithAt 41: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 41: [ RUN ] StringTableTest.CanAccessWithBracket 41: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 41: [ RUN ] StringTableTest.ThrowsOutOfRange 41: [ OK ] StringTableTest.ThrowsOutOfRange (7 ms) 41: [ RUN ] StringTableTest.StringCompareIsCorrect 41: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 41: [ RUN ] StringTableTest.AddTwoDistinctEntries 41: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 41: [ RUN ] StringTableTest.TryToAddDuplicates 41: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 41: [ RUN ] StringTableTest.AddLargeNumberOfEntries 41: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 41: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 41: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 41: [ RUN ] StringTableTest.CanWriteToBuffer 41: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 41: [ RUN ] StringTableTest.Roundtrip 41: [ OK ] StringTableTest.Roundtrip (0 ms) 41: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 41: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 41: [ RUN ] StringTableTest.CanCopyToLegacyTable 41: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 41: [----------] 13 tests from StringTableTest (17 ms total) 41: 41: [----------] 6 tests from LegacySymtabTest 41: [ RUN ] LegacySymtabTest.EmptyOnOpen 41: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 41: [ RUN ] LegacySymtabTest.AddSingleEntry 41: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 41: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 41: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 41: [ RUN ] LegacySymtabTest.TryToAddDuplicates 41: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 41: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 41: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 41: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 41: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 41: [----------] 6 tests from LegacySymtabTest (0 ms total) 41: 41: [----------] 5 tests from TopSortTest 41: [ RUN ] TopSortTest.WorksOnEmptyIdef 41: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 41: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 41: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 41: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 41: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 41: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 41: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 41: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 41: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 41: [----------] 5 tests from TopSortTest (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 40 tests from 7 test suites ran. (18 ms total) 41: [ PASSED ] 40 tests. 41/81 Test #41: TopologyTest ................................... Passed 0.06 sec test 42 Start 42: PullTest 42: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/PullTest.xml" 42: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/pulling/tests 42: Test timeout computed to be: 30 42: [==========] Running 8 tests from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 8 tests from PullTest 42: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 42: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (7 ms) 42: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 42: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 42: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 42: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 42: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 42: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 42: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 42: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 42: [ RUN ] PullTest.TransformationCoordSimple 42: [ OK ] PullTest.TransformationCoordSimple (43 ms) 42: [ RUN ] PullTest.TransformationCoordAdvanced 42: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 42: [ RUN ] PullTest.TransformationCoordDummyExpression 42: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 42: [----------] 8 tests from PullTest (51 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 8 tests from 1 test suite ran. (51 ms total) 42: [ PASSED ] 8 tests. 42/81 Test #42: PullTest ....................................... Passed 0.11 sec test 43 Start 43: SimdUnitTests 43: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/SimdUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/simd/tests 43: Test timeout computed to be: 30 43: [==========] Running 288 tests from 22 test suites. 43: [----------] Global test environment set-up. 43: [----------] 9 tests from SimdBootstrapTest 43: [ RUN ] SimdBootstrapTest.loadStore 43: [ OK ] SimdBootstrapTest.loadStore (0 ms) 43: [ RUN ] SimdBootstrapTest.loadU 43: [ OK ] SimdBootstrapTest.loadU (0 ms) 43: [ RUN ] SimdBootstrapTest.storeU 43: [ OK ] SimdBootstrapTest.storeU (0 ms) 43: [ RUN ] SimdBootstrapTest.loadStoreI 43: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 43: [ RUN ] SimdBootstrapTest.loadUI 43: [ OK ] SimdBootstrapTest.loadUI (0 ms) 43: [ RUN ] SimdBootstrapTest.storeUI 43: [ OK ] SimdBootstrapTest.storeUI (0 ms) 43: [ RUN ] SimdBootstrapTest.simd4LoadStore 43: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 43: [ RUN ] SimdBootstrapTest.simd4LoadU 43: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 43: [ RUN ] SimdBootstrapTest.simd4StoreU 43: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 43: [----------] 9 tests from SimdBootstrapTest (0 ms total) 43: 43: [----------] 41 tests from SimdScalarTest 43: [ RUN ] SimdScalarTest.load 43: [ OK ] SimdScalarTest.load (0 ms) 43: [ RUN ] SimdScalarTest.loadU 43: [ OK ] SimdScalarTest.loadU (0 ms) 43: [ RUN ] SimdScalarTest.store 43: [ OK ] SimdScalarTest.store (0 ms) 43: [ RUN ] SimdScalarTest.storeU 43: [ OK ] SimdScalarTest.storeU (0 ms) 43: [ RUN ] SimdScalarTest.setZero 43: [ OK ] SimdScalarTest.setZero (0 ms) 43: [ RUN ] SimdScalarTest.andNot 43: [ OK ] SimdScalarTest.andNot (0 ms) 43: [ RUN ] SimdScalarTest.fma 43: [ OK ] SimdScalarTest.fma (0 ms) 43: [ RUN ] SimdScalarTest.fms 43: [ OK ] SimdScalarTest.fms (0 ms) 43: [ RUN ] SimdScalarTest.fnma 43: [ OK ] SimdScalarTest.fnma (0 ms) 43: [ RUN ] SimdScalarTest.fnms 43: [ OK ] SimdScalarTest.fnms (0 ms) 43: [ RUN ] SimdScalarTest.maskAdd 43: [ OK ] SimdScalarTest.maskAdd (0 ms) 43: [ RUN ] SimdScalarTest.maskzMul 43: [ OK ] SimdScalarTest.maskzMul (0 ms) 43: [ RUN ] SimdScalarTest.maskzFma 43: [ OK ] SimdScalarTest.maskzFma (0 ms) 43: [ RUN ] SimdScalarTest.abs 43: [ OK ] SimdScalarTest.abs (0 ms) 43: [ RUN ] SimdScalarTest.max 43: [ OK ] SimdScalarTest.max (0 ms) 43: [ RUN ] SimdScalarTest.min 43: [ OK ] SimdScalarTest.min (0 ms) 43: [ RUN ] SimdScalarTest.round 43: [ OK ] SimdScalarTest.round (0 ms) 43: [ RUN ] SimdScalarTest.trunc 43: [ OK ] SimdScalarTest.trunc (0 ms) 43: [ RUN ] SimdScalarTest.reduce 43: [ OK ] SimdScalarTest.reduce (0 ms) 43: [ RUN ] SimdScalarTest.testBits 43: [ OK ] SimdScalarTest.testBits (0 ms) 43: [ RUN ] SimdScalarTest.anyTrue 43: [ OK ] SimdScalarTest.anyTrue (0 ms) 43: [ RUN ] SimdScalarTest.selectByMask 43: [ OK ] SimdScalarTest.selectByMask (0 ms) 43: [ RUN ] SimdScalarTest.selectByNotMask 43: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 43: [ RUN ] SimdScalarTest.blend 43: [ OK ] SimdScalarTest.blend (0 ms) 43: [ RUN ] SimdScalarTest.cvtR2I 43: [ OK ] SimdScalarTest.cvtR2I (0 ms) 43: [ RUN ] SimdScalarTest.cvttR2I 43: [ OK ] SimdScalarTest.cvttR2I (0 ms) 43: [ RUN ] SimdScalarTest.cvtI2R 43: [ OK ] SimdScalarTest.cvtI2R (0 ms) 43: [ RUN ] SimdScalarTest.cvtF2D 43: [ OK ] SimdScalarTest.cvtF2D (0 ms) 43: [ RUN ] SimdScalarTest.cvtD2D 43: [ OK ] SimdScalarTest.cvtD2D (0 ms) 43: [ RUN ] SimdScalarTest.loadI 43: [ OK ] SimdScalarTest.loadI (0 ms) 43: [ RUN ] SimdScalarTest.loadUI 43: [ OK ] SimdScalarTest.loadUI (0 ms) 43: [ RUN ] SimdScalarTest.storeI 43: [ OK ] SimdScalarTest.storeI (0 ms) 43: [ RUN ] SimdScalarTest.storeUI 43: [ OK ] SimdScalarTest.storeUI (0 ms) 43: [ RUN ] SimdScalarTest.andNotI 43: [ OK ] SimdScalarTest.andNotI (0 ms) 43: [ RUN ] SimdScalarTest.testBitsI 43: [ OK ] SimdScalarTest.testBitsI (0 ms) 43: [ RUN ] SimdScalarTest.selectByMaskI 43: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 43: [ RUN ] SimdScalarTest.selectByNotMaskI 43: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 43: [ RUN ] SimdScalarTest.blendI 43: [ OK ] SimdScalarTest.blendI (0 ms) 43: [ RUN ] SimdScalarTest.cvtB2IB 43: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 43: [ RUN ] SimdScalarTest.cvtIB2B 43: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 43: [ RUN ] SimdScalarTest.expandScalarsToTriplets 43: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 43: [----------] 41 tests from SimdScalarTest (0 ms total) 43: 43: [----------] 8 tests from SimdScalarUtilTest 43: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 43: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 43: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 43: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 43: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 43: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 43: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 43: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 43: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 43: 43: [----------] 37 tests from SimdScalarMathTest 43: [ RUN ] SimdScalarMathTest.copysign 43: [ OK ] SimdScalarMathTest.copysign (0 ms) 43: [ RUN ] SimdScalarMathTest.invsqrtPair 43: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 43: [ RUN ] SimdScalarMathTest.inv 43: [ OK ] SimdScalarMathTest.inv (0 ms) 43: [ RUN ] SimdScalarMathTest.maskzInvsqrt 43: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 43: [ RUN ] SimdScalarMathTest.log 43: [ OK ] SimdScalarMathTest.log (0 ms) 43: [ RUN ] SimdScalarMathTest.exp2 43: [ OK ] SimdScalarMathTest.exp2 (0 ms) 43: [ RUN ] SimdScalarMathTest.exp 43: [ OK ] SimdScalarMathTest.exp (0 ms) 43: [ RUN ] SimdScalarMathTest.erf 43: [ OK ] SimdScalarMathTest.erf (0 ms) 43: [ RUN ] SimdScalarMathTest.erfc 43: [ OK ] SimdScalarMathTest.erfc (0 ms) 43: [ RUN ] SimdScalarMathTest.sincos 43: [ OK ] SimdScalarMathTest.sincos (0 ms) 43: [ RUN ] SimdScalarMathTest.sin 43: [ OK ] SimdScalarMathTest.sin (0 ms) 43: [ RUN ] SimdScalarMathTest.cos 43: [ OK ] SimdScalarMathTest.cos (0 ms) 43: [ RUN ] SimdScalarMathTest.tan 43: [ OK ] SimdScalarMathTest.tan (0 ms) 43: [ RUN ] SimdScalarMathTest.asin 43: [ OK ] SimdScalarMathTest.asin (0 ms) 43: [ RUN ] SimdScalarMathTest.acos 43: [ OK ] SimdScalarMathTest.acos (0 ms) 43: [ RUN ] SimdScalarMathTest.atan 43: [ OK ] SimdScalarMathTest.atan (0 ms) 43: [ RUN ] SimdScalarMathTest.atan2 43: [ OK ] SimdScalarMathTest.atan2 (0 ms) 43: [ RUN ] SimdScalarMathTest.pmeForceCorrection 43: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 43: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 43: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 43: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 43: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.invSingleAccuracy 43: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 43: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.logSingleAccuracy 43: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 43: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.expSingleAccuracy 43: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 43: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 43: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 43: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 43: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 43: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 43: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 43: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 43: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 43: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 43: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 43: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 43: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 43: [----------] 37 tests from SimdScalarMathTest (0 ms total) 43: 43: [----------] 1 test from SimdTest 43: [ RUN ] SimdTest.GmxAligned 43: [ OK ] SimdTest.GmxAligned (0 ms) 43: [----------] 1 test from SimdTest (0 ms total) 43: 43: [----------] 42 tests from SimdFloatingpointTest 43: [ RUN ] SimdFloatingpointTest.setZero 43: [ OK ] SimdFloatingpointTest.setZero (0 ms) 43: [ RUN ] SimdFloatingpointTest.set 43: [ OK ] SimdFloatingpointTest.set (0 ms) 43: [ RUN ] SimdFloatingpointTest.add 43: [ OK ] SimdFloatingpointTest.add (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskAdd 43: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 43: [ RUN ] SimdFloatingpointTest.sub 43: [ OK ] SimdFloatingpointTest.sub (0 ms) 43: [ RUN ] SimdFloatingpointTest.mul 43: [ OK ] SimdFloatingpointTest.mul (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzMul 43: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 43: [ RUN ] SimdFloatingpointTest.fma 43: [ OK ] SimdFloatingpointTest.fma (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzFma 43: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 43: [ RUN ] SimdFloatingpointTest.fms 43: [ OK ] SimdFloatingpointTest.fms (0 ms) 43: [ RUN ] SimdFloatingpointTest.fnma 43: [ OK ] SimdFloatingpointTest.fnma (0 ms) 43: [ RUN ] SimdFloatingpointTest.fnms 43: [ OK ] SimdFloatingpointTest.fnms (0 ms) 43: [ RUN ] SimdFloatingpointTest.abs 43: [ OK ] SimdFloatingpointTest.abs (0 ms) 43: [ RUN ] SimdFloatingpointTest.neg 43: [ OK ] SimdFloatingpointTest.neg (0 ms) 43: [ RUN ] SimdFloatingpointTest.and 43: [ OK ] SimdFloatingpointTest.and (0 ms) 43: [ RUN ] SimdFloatingpointTest.or 43: [ OK ] SimdFloatingpointTest.or (0 ms) 43: [ RUN ] SimdFloatingpointTest.xor 43: [ OK ] SimdFloatingpointTest.xor (0 ms) 43: [ RUN ] SimdFloatingpointTest.andNot 43: [ OK ] SimdFloatingpointTest.andNot (0 ms) 43: [ RUN ] SimdFloatingpointTest.max 43: [ OK ] SimdFloatingpointTest.max (0 ms) 43: [ RUN ] SimdFloatingpointTest.min 43: [ OK ] SimdFloatingpointTest.min (0 ms) 43: [ RUN ] SimdFloatingpointTest.round 43: [ OK ] SimdFloatingpointTest.round (0 ms) 43: [ RUN ] SimdFloatingpointTest.roundMode 43: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 43: [ RUN ] SimdFloatingpointTest.trunc 43: [ OK ] SimdFloatingpointTest.trunc (0 ms) 43: [ RUN ] SimdFloatingpointTest.frexp 43: [ OK ] SimdFloatingpointTest.frexp (0 ms) 43: [ RUN ] SimdFloatingpointTest.ldexp 43: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 43: [ RUN ] SimdFloatingpointTest.rsqrt 43: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzRsqrt 43: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 43: [ RUN ] SimdFloatingpointTest.rcp 43: [ OK ] SimdFloatingpointTest.rcp (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzRcp 43: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 43: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 43: [ RUN ] SimdFloatingpointTest.selectByNotMask 43: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpNe 43: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpLe 43: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpLt 43: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 43: [ RUN ] SimdFloatingpointTest.testBits 43: [ OK ] SimdFloatingpointTest.testBits (0 ms) 43: [ RUN ] SimdFloatingpointTest.andB 43: [ OK ] SimdFloatingpointTest.andB (0 ms) 43: [ RUN ] SimdFloatingpointTest.orB 43: [ OK ] SimdFloatingpointTest.orB (0 ms) 43: [ RUN ] SimdFloatingpointTest.anyTrueB 43: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 43: [ RUN ] SimdFloatingpointTest.blend 43: [ OK ] SimdFloatingpointTest.blend (0 ms) 43: [ RUN ] SimdFloatingpointTest.reduce 43: [ OK ] SimdFloatingpointTest.reduce (0 ms) 43: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 43: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 43: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 43: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 43: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 43: 43: [----------] 16 tests from SimdFloatingpointUtilTest 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 43: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 43: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 43: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 43: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 43: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 43: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 43: 43: [----------] 23 tests from SimdIntegerTest 43: [ RUN ] SimdIntegerTest.setZero 43: [ OK ] SimdIntegerTest.setZero (0 ms) 43: [ RUN ] SimdIntegerTest.set 43: [ OK ] SimdIntegerTest.set (0 ms) 43: [ RUN ] SimdIntegerTest.add 43: [ OK ] SimdIntegerTest.add (0 ms) 43: [ RUN ] SimdIntegerTest.sub 43: [ OK ] SimdIntegerTest.sub (0 ms) 43: [ RUN ] SimdIntegerTest.mul 43: [ OK ] SimdIntegerTest.mul (0 ms) 43: [ RUN ] SimdIntegerTest.and 43: [ OK ] SimdIntegerTest.and (0 ms) 43: [ RUN ] SimdIntegerTest.andNot 43: [ OK ] SimdIntegerTest.andNot (0 ms) 43: [ RUN ] SimdIntegerTest.or 43: [ OK ] SimdIntegerTest.or (0 ms) 43: [ RUN ] SimdIntegerTest.xor 43: [ OK ] SimdIntegerTest.xor (0 ms) 43: [ RUN ] SimdIntegerTest.extract 43: [ OK ] SimdIntegerTest.extract (0 ms) 43: [ RUN ] SimdIntegerTest.cvtR2I 43: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 43: [ RUN ] SimdIntegerTest.cvttR2I 43: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 43: [ RUN ] SimdIntegerTest.cvtI2R 43: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 43: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 43: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 43: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 43: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 43: [ RUN ] SimdIntegerTest.cmpLt 43: [ OK ] SimdIntegerTest.cmpLt (0 ms) 43: [ RUN ] SimdIntegerTest.testBits 43: [ OK ] SimdIntegerTest.testBits (0 ms) 43: [ RUN ] SimdIntegerTest.andB 43: [ OK ] SimdIntegerTest.andB (0 ms) 43: [ RUN ] SimdIntegerTest.orB 43: [ OK ] SimdIntegerTest.orB (0 ms) 43: [ RUN ] SimdIntegerTest.anyTrue 43: [ OK ] SimdIntegerTest.anyTrue (0 ms) 43: [ RUN ] SimdIntegerTest.blend 43: [ OK ] SimdIntegerTest.blend (0 ms) 43: [ RUN ] SimdIntegerTest.cvtB2IB 43: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 43: [ RUN ] SimdIntegerTest.cvtIB2B 43: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 43: [----------] 23 tests from SimdIntegerTest (0 ms total) 43: 43: [----------] 56 tests from SimdMathTest 43: [ RUN ] SimdMathTest.generateTestPointsFloat 43: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 43: [ RUN ] SimdMathTest.copysign 43: [ OK ] SimdMathTest.copysign (0 ms) 43: [ RUN ] SimdMathTest.invsqrt 43: [ OK ] SimdMathTest.invsqrt (0 ms) 43: [ RUN ] SimdMathTest.maskzInvsqrt 43: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 43: [ RUN ] SimdMathTest.invsqrtPair 43: [ OK ] SimdMathTest.invsqrtPair (0 ms) 43: [ RUN ] SimdMathTest.sqrt 43: [ OK ] SimdMathTest.sqrt (0 ms) 43: [ RUN ] SimdMathTest.sqrtUnsafe 43: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 43: [ RUN ] SimdMathTest.inv 43: [ OK ] SimdMathTest.inv (10 ms) 43: [ RUN ] SimdMathTest.maskzInv 43: [ OK ] SimdMathTest.maskzInv (0 ms) 43: [ RUN ] SimdMathTest.cbrt 43: [ OK ] SimdMathTest.cbrt (0 ms) 43: [ RUN ] SimdMathTest.invcbrt 43: [ OK ] SimdMathTest.invcbrt (1 ms) 43: [ RUN ] SimdMathTest.log2 43: [ OK ] SimdMathTest.log2 (0 ms) 43: [ RUN ] SimdMathTest.log 43: [ OK ] SimdMathTest.log (0 ms) 43: [ RUN ] SimdMathTest.exp2 43: [ OK ] SimdMathTest.exp2 (8 ms) 43: [ RUN ] SimdMathTest.exp2Unsafe 43: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 43: [ RUN ] SimdMathTest.exp 43: [ OK ] SimdMathTest.exp (2 ms) 43: [ RUN ] SimdMathTest.expUnsafe 43: [ OK ] SimdMathTest.expUnsafe (0 ms) 43: [ RUN ] SimdMathTest.pow 43: [ OK ] SimdMathTest.pow (0 ms) 43: [ RUN ] SimdMathTest.powUnsafe 43: [ OK ] SimdMathTest.powUnsafe (0 ms) 43: [ RUN ] SimdMathTest.erf 43: [ OK ] SimdMathTest.erf (10 ms) 43: [ RUN ] SimdMathTest.erfc 43: [ OK ] SimdMathTest.erfc (2 ms) 43: [ RUN ] SimdMathTest.sin 43: [ OK ] SimdMathTest.sin (1 ms) 43: [ RUN ] SimdMathTest.cos 43: [ OK ] SimdMathTest.cos (1 ms) 43: [ RUN ] SimdMathTest.tan 43: [ OK ] SimdMathTest.tan (1 ms) 43: [ RUN ] SimdMathTest.asin 43: [ OK ] SimdMathTest.asin (8 ms) 43: [ RUN ] SimdMathTest.acos 43: [ OK ] SimdMathTest.acos (0 ms) 43: [ RUN ] SimdMathTest.atan 43: [ OK ] SimdMathTest.atan (0 ms) 43: [ RUN ] SimdMathTest.atan2 43: [ OK ] SimdMathTest.atan2 (0 ms) 43: [ RUN ] SimdMathTest.pmeForceCorrection 43: [ OK ] SimdMathTest.pmeForceCorrection (1 ms) 43: [ RUN ] SimdMathTest.pmePotentialCorrection 43: [ OK ] SimdMathTest.pmePotentialCorrection (8 ms) 43: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 43: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 43: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.sqrtSingleAccuracy 43: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 43: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.invSingleAccuracy 43: [ OK ] SimdMathTest.invSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.cbrtSingleAccuracy 43: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 43: [ OK ] SimdMathTest.invcbrtSingleAccuracy (9 ms) 43: [ RUN ] SimdMathTest.log2SingleAccuracy 43: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.logSingleAccuracy 43: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.exp2SingleAccuracy 43: [ OK ] SimdMathTest.exp2SingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 43: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (4 ms) 43: [ RUN ] SimdMathTest.expSingleAccuracy 43: [ OK ] SimdMathTest.expSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 43: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.powSingleAccuracy 43: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 43: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.erfSingleAccuracy 43: [ OK ] SimdMathTest.erfSingleAccuracy (9 ms) 43: [ RUN ] SimdMathTest.erfcSingleAccuracy 43: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.sinSingleAccuracy 43: [ OK ] SimdMathTest.sinSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.cosSingleAccuracy 43: [ OK ] SimdMathTest.cosSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.tanSingleAccuracy 43: [ OK ] SimdMathTest.tanSingleAccuracy (10 ms) 43: [ RUN ] SimdMathTest.asinSingleAccuracy 43: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.acosSingleAccuracy 43: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.atanSingleAccuracy 43: [ OK ] SimdMathTest.atanSingleAccuracy (4 ms) 43: [ RUN ] SimdMathTest.atan2SingleAccuracy 43: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 43: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 43: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 43: [----------] 56 tests from SimdMathTest (135 ms total) 43: 43: [----------] 1 test from EmptyArrayRefTest 43: [ RUN ] EmptyArrayRefTest.IsEmpty 43: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 43: [----------] 1 test from EmptyArrayRefTest (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 43: 43: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefReadWriteTest/0.Assignment 43: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 43: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 43: 43: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefReadWriteTest/1.Assignment 43: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 43: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 43: 43: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefArithmeticTest/0.Basic 43: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 43: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 43: 43: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefArithmeticTest/1.Basic 43: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 43: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 43: 43: [----------] 3 tests from SimdVectorOperationsTest 43: [ RUN ] SimdVectorOperationsTest.iprod 43: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 43: [ RUN ] SimdVectorOperationsTest.norm2 43: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 43: [ RUN ] SimdVectorOperationsTest.cprod 43: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 43: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 43: 43: [----------] 32 tests from Simd4FloatingpointTest 43: [ RUN ] Simd4FloatingpointTest.setZero 43: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 43: [ RUN ] Simd4FloatingpointTest.set 43: [ OK ] Simd4FloatingpointTest.set (0 ms) 43: [ RUN ] Simd4FloatingpointTest.add 43: [ OK ] Simd4FloatingpointTest.add (0 ms) 43: [ RUN ] Simd4FloatingpointTest.sub 43: [ OK ] Simd4FloatingpointTest.sub (0 ms) 43: [ RUN ] Simd4FloatingpointTest.mul 43: [ OK ] Simd4FloatingpointTest.mul (0 ms) 43: [ RUN ] Simd4FloatingpointTest.fma 43: [ OK ] Simd4FloatingpointTest.fma (0 ms) 43: [ RUN ] Simd4FloatingpointTest.fms 43: [ OK ] Simd4FloatingpointTest.fms (0 ms) 43: [ RUN ] Simd4FloatingpointTest.fnma 43: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 43: [ RUN ] Simd4FloatingpointTest.fnms 43: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 43: [ RUN ] Simd4FloatingpointTest.abs 43: [ OK ] Simd4FloatingpointTest.abs (0 ms) 43: [ RUN ] Simd4FloatingpointTest.neg 43: [ OK ] Simd4FloatingpointTest.neg (0 ms) 43: [ RUN ] Simd4FloatingpointTest.and 43: [ OK ] Simd4FloatingpointTest.and (0 ms) 43: [ RUN ] Simd4FloatingpointTest.or 43: [ OK ] Simd4FloatingpointTest.or (0 ms) 43: [ RUN ] Simd4FloatingpointTest.xor 43: [ OK ] Simd4FloatingpointTest.xor (0 ms) 43: [ RUN ] Simd4FloatingpointTest.andNot 43: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 43: [ RUN ] Simd4FloatingpointTest.max 43: [ OK ] Simd4FloatingpointTest.max (0 ms) 43: [ RUN ] Simd4FloatingpointTest.min 43: [ OK ] Simd4FloatingpointTest.min (0 ms) 43: [ RUN ] Simd4FloatingpointTest.round 43: [ OK ] Simd4FloatingpointTest.round (0 ms) 43: [ RUN ] Simd4FloatingpointTest.trunc 43: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 43: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 43: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 43: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 43: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 43: [ RUN ] Simd4FloatingpointTest.selectByNotMask 43: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 43: [ RUN ] Simd4FloatingpointTest.cmpNe 43: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 43: [ RUN ] Simd4FloatingpointTest.cmpLe 43: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 43: [ RUN ] Simd4FloatingpointTest.cmpLt 43: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 43: [ RUN ] Simd4FloatingpointTest.andB 43: [ OK ] Simd4FloatingpointTest.andB (0 ms) 43: [ RUN ] Simd4FloatingpointTest.orB 43: [ OK ] Simd4FloatingpointTest.orB (0 ms) 43: [ RUN ] Simd4FloatingpointTest.anyTrue 43: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 43: [ RUN ] Simd4FloatingpointTest.blend 43: [ OK ] Simd4FloatingpointTest.blend (0 ms) 43: [ RUN ] Simd4FloatingpointTest.reduce 43: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 43: [ RUN ] Simd4FloatingpointTest.dotProduct 43: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 43: [ RUN ] Simd4FloatingpointTest.transpose 43: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 43: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 43: 43: [----------] 2 tests from Simd4MathTest 43: [ RUN ] Simd4MathTest.invsqrt 43: [ OK ] Simd4MathTest.invsqrt (0 ms) 43: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 43: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 43: [----------] 2 tests from Simd4MathTest (0 ms total) 43: 43: [----------] 1 test from Simd4VectorOperationsTest 43: [ RUN ] Simd4VectorOperationsTest.norm2 43: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 43: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 288 tests from 22 test suites ran. (138 ms total) 43: [ PASSED ] 288 tests. 43/81 Test #43: SimdUnitTests .................................. Passed 0.20 sec test 44 Start 44: CompatibilityHelpersTests 44: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/compat/tests 44: Test timeout computed to be: 30 44: [==========] Running 9 tests from 6 test suites. 44: [----------] Global test environment set-up. 44: [----------] 4 tests from TemplateMPTest 44: [ RUN ] TemplateMPTest.MpWithIndexInt 44: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 44: [ RUN ] TemplateMPTest.MpWithIndexIntBad 44: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 44: [ RUN ] TemplateMPTest.MpWithIndexBool 44: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 44: [ RUN ] TemplateMPTest.MpWithIndexEnum 44: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 44: [----------] 4 tests from TemplateMPTest (0 ms total) 44: 44: [----------] 1 test from NotNullConstruction 44: [ RUN ] NotNullConstruction.Works 44: [ OK ] NotNullConstruction.Works (0 ms) 44: [----------] 1 test from NotNullConstruction (0 ms total) 44: 44: [----------] 1 test from NotNullCasting 44: [ RUN ] NotNullCasting.Works 44: [ OK ] NotNullCasting.Works (0 ms) 44: [----------] 1 test from NotNullCasting (0 ms total) 44: 44: [----------] 1 test from NotNullAssignment 44: [ RUN ] NotNullAssignment.Works 44: [ OK ] NotNullAssignment.Works (0 ms) 44: [----------] 1 test from NotNullAssignment (0 ms total) 44: 44: [----------] 1 test from MakeNotNull 44: [ RUN ] MakeNotNull.Works 44: [ OK ] MakeNotNull.Works (0 ms) 44: [----------] 1 test from MakeNotNull (0 ms total) 44: 44: [----------] 1 test from NotNull 44: [ RUN ] NotNull.WorksInContainers 44: [ OK ] NotNull.WorksInContainers (0 ms) 44: [----------] 1 test from NotNull (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 9 tests from 6 test suites ran. (0 ms total) 44: [ PASSED ] 9 tests. 44/81 Test #44: CompatibilityHelpersTests ...................... Passed 0.04 sec test 45 Start 45: GmxAnaTest 45: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/GmxAnaTest.xml" 45: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxana/tests 45: Test timeout computed to be: 600 45: [==========] Running 22 tests from 4 test suites. 45: [----------] Global test environment set-up. 45: [----------] 5 tests from Entropy 45: [ RUN ] Entropy.Schlitter_300_NoLinear 45: [ OK ] Entropy.Schlitter_300_NoLinear (6 ms) 45: [ RUN ] Entropy.Schlitter_300_Linear 45: [ OK ] Entropy.Schlitter_300_Linear (3 ms) 45: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 45: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (3 ms) 45: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 45: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (4 ms) 45: [ RUN ] Entropy.QuasiHarmonic_200_Linear 45: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 45: [----------] 5 tests from Entropy (18 ms total) 45: 45: [----------] 1 test from GmxChiTest 45: [ RUN ] GmxChiTest.gmxchiWorksWithAll 45: 45: 10 residues with dihedrals found 45: 46 dihedrals found 45: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 45: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 45: j after resetting (nr. active dihedrals) = 46 45: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 45: Now calculating transitions... 45: Total number of transitions: 0 45: Now printing out transitions and OPs... 45: Now printing out rotamer occupancies... 45: Now calculating Chi product trajectories... 45: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 45: 45: gmx chi is deprecated. 45: See https://gitlab.com/gromacs/gromacs/-/issues/4108 if 45: you are interested in preserving it! 45: [ OK ] GmxChiTest.gmxchiWorksWithAll (2602 ms) 45: [----------] 1 test from GmxChiTest (2848 ms total) 45: 45: [----------] 10 tests from MindistTest 45: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.mindistWorksWithSingleAtoms (129 ms) 45: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 2: 'atom3' 45: Selected 3: 'atoms12' 45: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (29 ms) 45: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 45: [ RUN ] MindistTest.mindistPicksUpContacts 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.mindistPicksUpContacts (2 ms) 45: [ RUN ] MindistTest.ngWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: Selected 2: 'atom3' 45: [ OK ] MindistTest.ngWorks (0 ms) 45: [ RUN ] MindistTest.groupWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 3: 'atoms12' 45: Selected 2: 'atom3' 45: [ OK ] MindistTest.groupWorks (0 ms) 45: [ RUN ] MindistTest.maxDistWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 2: 'atom3' 45: Selected 3: 'atoms12' 45: [ OK ] MindistTest.maxDistWorks (0 ms) 45: [ RUN ] MindistTest.noPbcWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.noPbcWorks (0 ms) 45: [ RUN ] MindistTest.resPerTimeWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 3: 'atoms12' 45: Selected 2: 'atom3' 45: [ OK ] MindistTest.resPerTimeWorks (0 ms) 45: [ RUN ] MindistTest.matrixWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 5: 'atoms123' 45: Special case: making distance matrix between all atoms in group atoms123 45: [ OK ] MindistTest.matrixWorks (10 ms) 45: [----------] 10 tests from MindistTest (177 ms total) 45: 45: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: trr version: GMX_trn_file (single precision) 45: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (7 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (11 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (11 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 45: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (1 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 45: Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (13 ms) 45: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (46 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 22 tests from 4 test suites ran. (3090 ms total) 45: [ PASSED ] 22 tests. 45/81 Test #45: GmxAnaTest ..................................... Passed 3.14 sec test 46 Start 46: GmxPreprocessTests 46: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests 46: Test timeout computed to be: 1920 46: [==========] Running 90 tests from 11 test suites. 46: [----------] Global test environment set-up. 46: [----------] 4 tests from GenconfTest 46: [ RUN ] GenconfTest.nbox_Works 46: [ OK ] GenconfTest.nbox_Works (6 ms) 46: [ RUN ] GenconfTest.nbox_norenumber_Works 46: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms) 46: [ RUN ] GenconfTest.nbox_dist_Works 46: [ OK ] GenconfTest.nbox_dist_Works (9 ms) 46: [ RUN ] GenconfTest.nbox_rot_Works 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: [ OK ] GenconfTest.nbox_rot_Works (7 ms) 46: [----------] 4 tests from GenconfTest (25 ms total) 46: 46: [----------] 2 tests from GenionTest 46: [ RUN ] GenionTest.HighConcentrationIonPlacement 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 46: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 46: buffer. The cluster pair list does have a buffering effect, but choosing 46: a larger rlist might be necessary for good energy conservation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: Generating 1-4 interactions: fudge = 0.5 46: Number of degrees of freedom in T-Coupling group rest is 1308.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 46: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 46: Group 0 ( System) has 653 elements 46: Group 1 ( Water) has 648 elements 46: Group 2 ( SOL) has 648 elements 46: Group 3 ( non-Water) has 5 elements 46: Group 4 ( Other) has 5 elements 46: Group 5 ( METH) has 5 elements 46: Select a group: Number of (3-atomic) solvent molecules: 216 46: Using random seed 1997. 46: Replacing solvent molecule 56 (atom 168) with NA 46: Replacing solvent molecule 120 (atom 360) with NA 46: Replacing solvent molecule 182 (atom 546) with NA 46: Replacing solvent molecule 71 (atom 213) with NA 46: Replacing solvent molecule 189 (atom 567) with CL 46: Replacing solvent molecule 54 (atom 162) with CL 46: Replacing solvent molecule 155 (atom 465) with CL 46: Replacing solvent molecule 99 (atom 297) with CL 46: 46: Setting the LD random seed to -8787083 46: 46: Generated 331705 of the 331705 non-bonded parameter combinations 46: 46: Generated 331705 of the 331705 1-4 parameter combinations 46: 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: 46: Excluding 3 bonded neighbours molecule type 'methane' 46: Analysing residue names: 46: There are: 216 Water residues 46: There are: 1 Other residues 46: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 46: 46: This run will generate roughly 0 Mb of data 46: Will try to add 4 NA ions and 4 CL ions. 46: Select a continuous group of solvent molecules 46: Selected 1: 'Water' 46: [ OK ] GenionTest.HighConcentrationIonPlacement (1011 ms) 46: [ RUN ] GenionTest.NoIonPlacement 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 46: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 46: buffer. The cluster pair list does have a buffering effect, but choosing 46: a larger rlist might be necessary for good energy conservation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: Generating 1-4 interactions: fudge = 0.5 46: Number of degrees of freedom in T-Coupling group rest is 1308.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 46: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 46: No ions to add, will just copy input configuration. 46: Setting the LD random seed to -143679493 46: 46: Generated 331705 of the 331705 non-bonded parameter combinations 46: 46: Generated 331705 of the 331705 1-4 parameter combinations 46: 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: 46: Excluding 3 bonded neighbours molecule type 'methane' 46: Analysing residue names: 46: There are: 216 Water residues 46: There are: 1 Other residues 46: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 46: 46: This run will generate roughly 0 Mb of data 46: [ OK ] GenionTest.NoIonPlacement (608 ms) 46: [----------] 2 tests from GenionTest (1620 ms total) 46: 46: [----------] 1 test from GenRestrTest 46: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 46: 46: Reading structure file 46: Group 0 ( System) has 156 elements 46: Group 1 ( Protein) has 156 elements 46: Group 2 ( Protein-H) has 75 elements 46: Group 3 ( C-alpha) has 10 elements 46: Group 4 ( Backbone) has 30 elements 46: Group 5 ( MainChain) has 40 elements 46: Group 6 ( MainChain+Cb) has 49 elements 46: Group 7 ( MainChain+H) has 52 elements 46: Group 8 ( SideChain) has 104 elements 46: Group 9 ( SideChain-H) has 35 elements 46: Select a group: Select group to position restrain 46: Selected 3: 'C-alpha' 46: [ OK ] GenRestrTest.SimpleRestraintsGenerated (3 ms) 46: [----------] 1 test from GenRestrTest (3 ms total) 46: 46: [----------] 9 tests from PreprocessingAtomTypesTest 46: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 46: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 46: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 46: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 46: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 46: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 46: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 46: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 46: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 46: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 46: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 46: 46: [----------] 10 tests from PreprocessingBondAtomTypeTest 46: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 46: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 46: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 46: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 46: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 46: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 46: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 46: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 46: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 46: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 46: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 46: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 46: 46: [----------] 1 test from GromppDirectiveTest 46: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 46: Ignoring obsolete mdp entry 'title' 46: Generating 1-4 interactions: fudge = 0.5 46: 46: NOTE 1 [file directives.top, line 44]: 46: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 46: any other atom in the same moleculetype. Although technically this might 46: not cause issues in a simulation, this often means that the user forgot 46: to add a bond/potential/constraint or put multiple molecules in the same 46: moleculetype definition by mistake. Run with -v to get information for 46: each atom. 46: 46: Number of degrees of freedom in T-Coupling group rest is 9.00 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 46: NVE simulation: will use the initial temperature of 300.000 K for 46: determining the Verlet buffer size 46: 46: 46: There were 2 notes 46: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 46: Setting the LD random seed to -201859130 46: 46: Generated 10 of the 10 non-bonded parameter combinations 46: 46: Generated 10 of the 10 1-4 parameter combinations 46: 46: Excluding 0 bonded neighbours molecule type 'A' 46: 46: Setting gen_seed to -3162265 46: 46: Velocities were taken from a Maxwell distribution at 300 K 46: Analysing residue names: 46: There are: 1 Other residues 46: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 46: 46: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 46: 46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 46: 46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 46: 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: 46: This run will generate roughly 0 Mb of data 46: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (8 ms) 46: [----------] 1 test from GromppDirectiveTest (8 ms total) 46: 46: [----------] 5 tests from InsertMoleculesTest 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 46: Reading solute configuration 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 8 atoms)! 46: 46: Added 1 molecules (out of 1 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 46: 46: Output configuration contains 8 atoms in 4 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (7 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 2 atoms)! 46: Try 2 success (now 4 atoms)! 46: Try 3 success (now 6 atoms)! 46: Try 4 success (now 8 atoms)! 46: Try 5 success (now 10 atoms)! 46: 46: Added 5 molecules (out of 5 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 46: 46: Output configuration contains 10 atoms in 10 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (2 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 46: Reading solute configuration 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 8 atoms)! 46: Try 2 success (now 10 atoms)! 46: 46: Added 2 molecules (out of 2 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 46: 46: Output configuration contains 10 atoms in 4 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (5 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 46: Reading solute configuration 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 650 atoms)! 46: Try 2 success (now 652 atoms)! 46: Try 3 success (now 654 atoms)! 46: Try 4 success (now 656 atoms)! 46: 46: Added 4 molecules (out of 4 requested) 46: Replaced 8 residues (24 atoms) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 46: 46: Output configuration contains 632 atoms in 212 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (18 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Read 4 positions from file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 46: 46: Try 1 success (now 2 atoms)! 46: Try 2 success (now 4 atoms)! 46: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 46: Try 13 success (now 6 atoms)! 46: 46: Added 3 molecules (out of 4 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 46: 46: Output configuration contains 6 atoms in 3 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (8 ms) 46: [----------] 5 tests from InsertMoleculesTest (42 ms total) 46: 46: [----------] 34 tests from GetIrTest 46: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 46: Ignoring obsolete mdp entry 'title' 46: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (5 ms) 46: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 46: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (13 ms) 46: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsKeyWithoutValue (7 ms) 46: [ RUN ] GetIrTest.RejectsValueWithoutKey 46: [ OK ] GetIrTest.RejectsValueWithoutKey (24 ms) 46: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 46: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (18 ms) 46: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (10 ms) 46: [ RUN ] GetIrTest.AcceptsEmptyLines 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsEmptyLines (5 ms) 46: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 46: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.MtsCheckNstcalcenergy (2 ms) 46: [ RUN ] GetIrTest.MtsCheckNstenergy 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 46: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (5) 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.MtsCheckNstenergy (4 ms) 46: [ RUN ] GetIrTest.MtsCheckNstpcouple 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 46: Pressure coupling incorrect number of values (I need exactly 1) 46: 46: 46: ERROR 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 46: Pressure coupling incorrect number of values (I need exactly 1) 46: 46: 46: ERROR 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: With multiple time stepping, nstpcouple should be a mutiple of mts-factor 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: 46: ERROR 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: The Berendsen barostat does not generate any strictly correct ensemble, 46: and should not be used for new production simulations (in our opinion). 46: For isotropic scaling we would recommend the C-rescale barostat that also 46: ensures fast relaxation without oscillations, and for anisotropic scaling 46: you likely want to use the Parrinello-Rahman barostat. 46: 46: 46: ERROR 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: compressibility must be > 0 when using pressure coupling Berendsen 46: 46: 46: [ OK ] GetIrTest.MtsCheckNstpcouple (3 ms) 46: [ RUN ] GetIrTest.MtsCheckNstdhdl 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstdhdl (5) 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: 46: ERROR 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: Lambda state must be set, either with init-lambda-state or with 46: init-lambda 46: 46: [ OK ] GetIrTest.MtsCheckNstdhdl (14 ms) 46: [ RUN ] GetIrTest.AcceptsElectricField 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsElectricField (12 ms) 46: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (17 ms) 46: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (12 ms) 46: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 46: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (16 ms) 46: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsImplicitSolventNo (8 ms) 46: [ RUN ] GetIrTest.RejectsImplicitSolventYes 46: [ OK ] GetIrTest.RejectsImplicitSolventYes (27 ms) 46: [ RUN ] GetIrTest.AcceptsMimic 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsMimic (11 ms) 46: [ RUN ] GetIrTest.AcceptsTransformationCoord 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 46: pull-coord2 has a non-zero force constant and is also referenced in 46: pull-coord1-expression. Make sure that this is intended. In most use 46: cases, the pull coordinates referenced by a transformation coordinate 46: should have their force constant set to zero. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsTransformationCoord (17 ms) 46: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 46: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (3 ms) 46: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 46: pull-coord2 can not use pull-coord1 in the transformation since this is a 46: constraint 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (11 ms) 46: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 46: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 46: 'transformation' 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (7 ms) 46: [ RUN ] GetIrTest.MissingTransformationCoordExpression 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 46: pull-coord1-expression not set for pull coordinate of geometry 46: 'transformation' 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.MissingTransformationCoordExpression (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (10 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (10 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 46: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 46: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 46: in total 100001 steps. This is not compatible with using soft-core 46: potentials. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (10 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 46: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 46: won't change anymore after step 100000 until the end of the simulation 46: after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 46: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 46: won't change anymore after step 100000 until the end of the simulation 46: after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 46: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 46: components won't change anymore after step 100000 until the end of the 46: simulation after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (10 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 46: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 46: components won't change anymore after step 100000 until the end of the 46: simulation after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (6 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (10 ms) 46: [----------] 34 tests from GetIrTest (333 ms total) 46: 46: [----------] 5 tests from SolvateTest 46: [ RUN ] SolvateTest.cs_box_Works 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 1x1x1 boxes 46: Solvent box contains 270 atoms in 90 residues 46: Removed 129 solvent atoms due to solvent-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 47 residues 46: Generated solvent containing 141 atoms in 47 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 46: 46: Output configuration contains 141 atoms in 47 residues 46: Volume : 1.331 (nm^3) 46: Density : 1056.36 (g/l) 46: Number of solvent molecules: 47 46: 46: [ OK ] SolvateTest.cs_box_Works (41 ms) 46: [ RUN ] SolvateTest.cs_cp_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 2x2x2 boxes 46: Solvent box contains 3660 atoms in 1220 residues 46: Removed 987 solvent atoms due to solvent-solvent overlap 46: Removed 15 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 886 residues 46: Generated solvent containing 2658 atoms in 886 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 46: 46: Output configuration contains 2664 atoms in 888 residues 46: Volume : 27.2709 (nm^3) 46: Density : 974.777 (g/l) 46: Number of solvent molecules: 886 46: 46: [ OK ] SolvateTest.cs_cp_Works (122 ms) 46: [ RUN ] SolvateTest.cs_cp_p_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 2x2x2 boxes 46: Solvent box contains 3660 atoms in 1220 residues 46: Removed 987 solvent atoms due to solvent-solvent overlap 46: Removed 15 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 886 residues 46: Generated solvent containing 2658 atoms in 886 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 46: 46: Output configuration contains 2664 atoms in 888 residues 46: Volume : 27.2709 (nm^3) 46: Density : 974.777 (g/l) 46: Number of solvent molecules: 886 46: 46: Processing topology 46: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 46: [ OK ] SolvateTest.cs_cp_p_Works (124 ms) 46: [ RUN ] SolvateTest.shell_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 2x2x2 boxes 46: Solvent box contains 3660 atoms in 1220 residues 46: Removed 987 solvent atoms due to solvent-solvent overlap 46: Removed 1902 solvent atoms more than 1.000000 nm from solute. 46: Removed 15 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 252 residues 46: Generated solvent containing 756 atoms in 252 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 46: 46: Output configuration contains 762 atoms in 254 residues 46: Volume : 27.2709 (nm^3) 46: Density : 279.3 (g/l) 46: Number of solvent molecules: 252 46: 46: [ OK ] SolvateTest.shell_Works (60 ms) 46: [ RUN ] SolvateTest.update_Topology_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 3x3x3 boxes 46: Solvent box contains 14952 atoms in 4984 residues 46: Removed 2787 solvent atoms due to solvent-solvent overlap 46: Removed 30 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 2 different molecule types: 46: HOH ( 3 atoms): 1876 residues 46: SOL ( 3 atoms): 2169 residues 46: Generated solvent containing 0 atoms in 0 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 46: 46: Output configuration contains 12141 atoms in 4047 residues 46: Volume : 125 (nm^3) 46: Density : 968.963 (g/l) 46: Number of solvent molecules: 4045 46: 46: Processing topology 46: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 46: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 46: [ OK ] SolvateTest.update_Topology_Works (554 ms) 46: [----------] 5 tests from SolvateTest (904 ms total) 46: 46: [----------] 1 test from TopDirTests 46: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 46: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 46: [----------] 1 test from TopDirTests (0 ms total) 46: 46: [----------] 18 tests from SinglePeptideFragments/EditconfTest 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (26 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (13 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (15 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (29 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (8 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (19 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (31 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (8 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (12 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (9 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (11 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (11 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (2 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (10 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (6 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (9 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (7 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (2 ms) 46: [----------] 18 tests from SinglePeptideFragments/EditconfTest (243 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 90 tests from 11 test suites ran. (3181 ms total) 46: [ PASSED ] 90 tests. 46/81 Test #46: GmxPreprocessTests ............................. Passed 3.22 sec test 47 Start 47: Pdb2gmx1Test 47: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 47: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests 47: Test timeout computed to be: 1920 47: [==========] Running 30 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 30 tests from Oplsaa/Pdb2gmxTest 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 0 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (271 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 0 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (190 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 0 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (165 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 0 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (155 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 0 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (648 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Marked 124 virtual sites 47: Added 16 dummy masses 47: Added 26 new constraints 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 130 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (170 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Marked 132 virtual sites 47: Added 10 dummy masses 47: Added 19 new constraints 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 133 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (179 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Marked 123 virtual sites 47: Added 22 dummy masses 47: Added 35 new constraints 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 132 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (171 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Marked 111 virtual sites 47: Added 18 dummy masses 47: Added 31 new constraints 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 116 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (149 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Marked 447 virtual sites 47: Added 58 dummy masses 47: Added 101 new constraints 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 462 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (761 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 0 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (77 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 0 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (80 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 0 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (69 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 0 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (60 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 0 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (273 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Marked 124 virtual sites 47: Added 16 dummy masses 47: Added 26 new constraints 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 130 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (113 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Marked 132 virtual sites 47: Added 10 dummy masses 47: Added 19 new constraints 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 133 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (77 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Marked 123 virtual sites 47: Added 22 dummy masses 47: Added 35 new constraints 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 132 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (92 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Marked 111 virtual sites 47: Added 18 dummy masses 47: Added 31 new constraints 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 116 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (72 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Marked 447 virtual sites 47: Added 58 dummy masses 47: Added 101 new constraints 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 462 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (323 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 0 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (63 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 0 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (74 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 0 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 0 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (58 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 0 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (312 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Marked 124 virtual sites 47: Added 16 dummy masses 47: Added 26 new constraints 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 130 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (143 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Marked 132 virtual sites 47: Added 10 dummy masses 47: Added 19 new constraints 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 133 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (102 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Marked 123 virtual sites 47: Added 22 dummy masses 47: Added 35 new constraints 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 132 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (93 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Marked 111 virtual sites 47: Added 18 dummy masses 47: Added 31 new constraints 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 116 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (218 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Marked 447 virtual sites 47: Added 58 dummy masses 47: Added 101 new constraints 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 462 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (406 ms) 47: [----------] 30 tests from Oplsaa/Pdb2gmxTest (5644 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 30 tests from 1 test suite ran. (5644 ms total) 47: [ PASSED ] 30 tests. 47/81 Test #47: Pdb2gmx1Test ................................... Passed 5.69 sec test 48 Start 48: Pdb2gmx2Test 48: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 48: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests 48: Test timeout computed to be: 1920 48: [==========] Running 40 tests from 2 test suites. 48: [----------] Global test environment set-up. 48: [----------] 20 tests from G43a1/Pdb2gmxTest 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (107 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (78 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (65 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (60 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (174 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 37 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 37 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (68 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 53 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 51 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (90 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 36 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 36 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (72 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 33 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 31 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (94 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 146 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 137 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (217 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (76 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (103 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (230 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (166 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (178 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 37 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 37 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (79 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 53 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 51 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (183 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 36 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 36 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (162 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 33 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 31 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (151 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 146 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 137 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (412 ms) 48: [----------] 20 tests from G43a1/Pdb2gmxTest (2776 ms total) 48: 48: [----------] 20 tests from G53a6/Pdb2gmxTest 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (225 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (192 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (174 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (164 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (406 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 39 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 39 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (172 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 57 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 55 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (193 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 38 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 38 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (173 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 35 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 33 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (83 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 150 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 141 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (477 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (123 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (75 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (69 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (118 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (353 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 39 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 39 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (119 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 57 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 55 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (263 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 38 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 38 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (145 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 35 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 33 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (90 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 150 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 141 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (215 ms) 48: [----------] 20 tests from G53a6/Pdb2gmxTest (3854 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 40 tests from 2 test suites ran. (6631 ms total) 48: [ PASSED ] 40 tests. 48/81 Test #48: Pdb2gmx2Test ................................... Passed 6.68 sec test 49 Start 49: Pdb2gmx3Test 49: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 49: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/gmxpreprocess/tests 49: Test timeout computed to be: 1920 49: [==========] Running 39 tests from 6 test suites. 49: [----------] Global test environment set-up. 49: [----------] 10 tests from Amber/Pdb2gmxTest 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 653 pairs 49: Before cleaning: 691 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 255, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 691 dihedrals, 51 impropers, 457 angles 49: 650 pairs, 254 bonds and 0 virtual sites 49: 49: Total mass 1846.132 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (204 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 748 pairs 49: Before cleaning: 788 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 291, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 788 dihedrals, 72 impropers, 516 angles 49: 736 pairs, 290 bonds and 0 virtual sites 49: 49: Total mass 2088.366 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (160 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 676 pairs 49: Before cleaning: 727 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 262, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 727 dihedrals, 56 impropers, 472 angles 49: 667 pairs, 261 bonds and 0 virtual sites 49: 49: Total mass 1861.124 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (77 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 603 pairs 49: Before cleaning: 634 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 233, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 634 dihedrals, 48 impropers, 419 angles 49: 597 pairs, 232 bonds and 0 virtual sites 49: 49: Total mass 1662.888 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (81 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 2499 pairs 49: Before cleaning: 2631 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 952, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2631 dihedrals, 208 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 0 virtual sites 49: 49: Total mass 6908.576 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (292 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 124 virtual sites 49: Added 16 dummy masses 49: Added 26 new constraints 49: Before cleaning: 653 pairs 49: Before cleaning: 691 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 255, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 691 dihedrals, 51 impropers, 457 angles 49: 650 pairs, 254 bonds and 130 virtual sites 49: 49: Total mass 1846.132 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (79 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 132 virtual sites 49: Added 10 dummy masses 49: Added 19 new constraints 49: Before cleaning: 748 pairs 49: Before cleaning: 788 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 291, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 788 dihedrals, 72 impropers, 516 angles 49: 736 pairs, 290 bonds and 133 virtual sites 49: 49: Total mass 2088.366 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (84 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 123 virtual sites 49: Added 22 dummy masses 49: Added 35 new constraints 49: Before cleaning: 676 pairs 49: Before cleaning: 727 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 262, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 727 dihedrals, 56 impropers, 472 angles 49: 667 pairs, 261 bonds and 132 virtual sites 49: 49: Total mass 1861.124 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (82 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 111 virtual sites 49: Added 18 dummy masses 49: Added 31 new constraints 49: Before cleaning: 603 pairs 49: Before cleaning: 634 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 233, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 634 dihedrals, 48 impropers, 419 angles 49: 597 pairs, 232 bonds and 116 virtual sites 49: 49: Total mass 1662.888 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (78 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 447 virtual sites 49: Added 58 dummy masses 49: Added 101 new constraints 49: Before cleaning: 2499 pairs 49: Before cleaning: 2631 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 952, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2631 dihedrals, 208 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 462 virtual sites 49: 49: Total mass 6908.576 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (314 ms) 49: [----------] 10 tests from Amber/Pdb2gmxTest (1457 ms total) 49: 49: [----------] 1 test from AmberTip4p/Pdb2gmxTest 49: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 49: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 2 4 (only water) 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (4 atoms, 2 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 2 residues with 8 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 4, now 4 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 2 angles 49: 0 pairs, 4 bonds and 0 virtual sites 49: 49: Total mass 36.032 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 49: 49: The Amber99sb-ildn force field and the tip4p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (36 ms) 49: [----------] 1 test from AmberTip4p/Pdb2gmxTest (36 ms total) 49: 49: [----------] 12 tests from Charmm/Pdb2gmxTest 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 653 pairs 49: Before cleaning: 663 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 254, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 663 dihedrals, 48 impropers, 457 angles 49: 650 pairs, 254 bonds and 0 virtual sites 49: 49: Total mass 1846.115 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (198 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 748 pairs 49: Before cleaning: 778 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus PHE-33: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 290, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 778 dihedrals, 49 impropers, 516 angles 49: 736 pairs, 290 bonds and 0 virtual sites 49: 49: Total mass 2088.361 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (142 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 676 pairs 49: Before cleaning: 696 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: Start terminus ALA-34: NH3+ 49: End terminus ALA-49: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 261, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 696 dihedrals, 39 impropers, 472 angles 49: 667 pairs, 261 bonds and 0 virtual sites 49: 49: Total mass 1861.130 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (80 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 603 pairs 49: Before cleaning: 618 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: Start terminus LYS-50: NH3+ 49: End terminus PRO-65: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 232, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 618 dihedrals, 38 impropers, 419 angles 49: 597 pairs, 232 bonds and 0 virtual sites 49: 49: Total mass 1662.885 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (92 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 2499 pairs 49: Before cleaning: 2524 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: Start terminus ASN-24: NH3+ 49: End terminus ARG-81: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 951, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 56 cmap torsion pairs 49: 49: There are 2524 dihedrals, 149 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 0 virtual sites 49: 49: Total mass 6908.566 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (304 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 39 pairs 49: Before cleaning: 39 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb... 49: Read 'GLU', 9 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 49: 49: chain #res #atoms 49: 49: 1 'X' 1 9 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'X' (9 atoms, 1 residues) 49: 49: Identified residue GLU1 as a starting terminus. 49: 49: Identified residue GLU1 as a ending terminus. 49: Start terminus GLU-1: NH3+ 49: End terminus GLU-1: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 1 residues with 18 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 17, now 17 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 39 dihedrals, 2 impropers, 30 angles 49: 39 pairs, 17 bonds and 0 virtual sites 49: 49: Total mass 146.123 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (36 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 124 virtual sites 49: Added 16 dummy masses 49: Added 26 new constraints 49: Before cleaning: 653 pairs 49: Before cleaning: 663 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 254, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 663 dihedrals, 48 impropers, 457 angles 49: 650 pairs, 254 bonds and 130 virtual sites 49: 49: Total mass 1846.115 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (105 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 132 virtual sites 49: Added 10 dummy masses 49: Added 19 new constraints 49: Before cleaning: 748 pairs 49: Before cleaning: 778 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus PHE-33: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 290, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 778 dihedrals, 49 impropers, 516 angles 49: 736 pairs, 290 bonds and 133 virtual sites 49: 49: Total mass 2088.361 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (101 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 123 virtual sites 49: Added 22 dummy masses 49: Added 35 new constraints 49: Before cleaning: 676 pairs 49: Before cleaning: 696 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: Start terminus ALA-34: NH3+ 49: End terminus ALA-49: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 261, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 696 dihedrals, 39 impropers, 472 angles 49: 667 pairs, 261 bonds and 132 virtual sites 49: 49: Total mass 1861.130 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (107 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 111 virtual sites 49: Added 18 dummy masses 49: Added 31 new constraints 49: Before cleaning: 603 pairs 49: Before cleaning: 618 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: Start terminus LYS-50: NH3+ 49: End terminus PRO-65: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 232, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 618 dihedrals, 38 impropers, 419 angles 49: 597 pairs, 232 bonds and 116 virtual sites 49: 49: Total mass 1662.885 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (94 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 447 virtual sites 49: Added 58 dummy masses 49: Added 101 new constraints 49: Before cleaning: 2499 pairs 49: Before cleaning: 2524 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: Start terminus ASN-24: NH3+ 49: End terminus ARG-81: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 951, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 56 cmap torsion pairs 49: 49: There are 2524 dihedrals, 149 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 462 virtual sites 49: 49: Total mass 6908.566 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (445 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 8 virtual sites 49: Added 2 dummy masses 49: Added 3 new constraints 49: Before cleaning: 39 pairs 49: Before cleaning: 39 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb... 49: Read 'GLU', 9 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 49: 49: chain #res #atoms 49: 49: 1 'X' 1 9 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'X' (9 atoms, 1 residues) 49: 49: Identified residue GLU1 as a starting terminus. 49: 49: Identified residue GLU1 as a ending terminus. 49: Start terminus GLU-1: NH3+ 49: End terminus GLU-1: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 1 residues with 18 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 17, now 17 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 39 dihedrals, 2 impropers, 30 angles 49: 39 pairs, 17 bonds and 9 virtual sites 49: 49: Total mass 146.123 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (41 ms) 49: [----------] 12 tests from Charmm/Pdb2gmxTest (1754 ms total) 49: 49: [----------] 8 tests from ChainSep/Pdb2gmxTest 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 651 pairs 49: Before cleaning: 661 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on changing chain id only (ignoring TER records). 49: 49: Merged chains into joint molecule definitions at 2 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: Start terminus PHE-6: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 258 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 258, now 258 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 10 cmap torsion pairs 49: 49: There are 661 dihedrals, 46 impropers, 463 angles 49: 648 pairs, 258 bonds and 0 virtual sites 49: 49: Total mass 1882.146 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (81 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 123 pairs 49: Before cleaning: 123 dihedrals 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 10 donors and 7 acceptors were found. 49: There are 7 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS8 49: NE223 49: MET12 SD55 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 317 pairs 49: Before cleaning: 322 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on changing chain id only (ignoring TER records). 49: 49: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 4 28 49: 49: 2 'B' 7 58 49: 49: 3 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (28 atoms, 4 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 4 residues with 51 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 50, now 50 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2 cmap torsion pairs 49: 49: There are 123 dihedrals, 9 impropers, 88 angles 49: 123 pairs, 50 bonds and 0 virtual sites 49: 49: Total mass 434.421 a.m.u. 49: 49: Total charge -2.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (58 atoms, 7 residues) 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus PHE-6: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 7 residues with 124 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 125, now 125 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 5 cmap torsion pairs 49: 49: There are 322 dihedrals, 19 impropers, 227 angles 49: 314 pairs, 125 bonds and 0 virtual sites 49: 49: Total mass 846.083 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 51 atoms 4 residues 49: 49: Including chain 2 in system: 124 atoms 7 residues 49: 49: Including chain 3 in system: 83 atoms 5 residues 49: 49: Now there are 258 atoms and 16 residues 49: 49: Total mass in system 1882.146 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (69 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 651 pairs 49: Before cleaning: 661 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records only (ignoring chain id). 49: 49: Merged chains into joint molecule definitions at 2 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ILE-9: COO- 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 258 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 258, now 258 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 10 cmap torsion pairs 49: 49: There are 661 dihedrals, 46 impropers, 463 angles 49: 648 pairs, 258 bonds and 0 virtual sites 49: 49: Total mass 1882.146 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (83 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 10 donors and 12 acceptors were found. 49: There are 13 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 49: SG9 49: HIS8 NE251 1.055 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 288 pairs 49: Before cleaning: 293 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 152 pairs 49: Before cleaning: 152 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records only (ignoring chain id). 49: 49: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 8 61 49: 49: 2 'B' 3 25 49: 49: 3 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (61 atoms, 8 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ILE-9: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 8 residues with 114 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 115, now 115 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 6 cmap torsion pairs 49: 49: There are 293 dihedrals, 23 impropers, 203 angles 49: 285 pairs, 115 bonds and 0 virtual sites 49: 49: Total mass 888.952 a.m.u. 49: 49: Total charge -2.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (25 atoms, 3 residues) 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 61 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 60, now 60 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 152 dihedrals, 5 impropers, 112 angles 49: 152 pairs, 60 bonds and 0 virtual sites 49: 49: Total mass 391.552 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 114 atoms 8 residues 49: 49: Including chain 2 in system: 61 atoms 3 residues 49: 49: Including chain 3 in system: 83 atoms 5 residues 49: 49: Now there are 258 atoms and 16 residues 49: 49: Total mass in system 1882.146 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (67 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 650 pairs 49: Before cleaning: 660 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Merged chains into joint molecule definitions at 3 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: Start terminus PHE-6: NH3+ 49: End terminus ILE-9: COO- 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 261 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 260, now 260 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 8 cmap torsion pairs 49: 49: There are 660 dihedrals, 45 impropers, 466 angles 49: 647 pairs, 260 bonds and 0 virtual sites 49: 49: Total mass 1900.162 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (82 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 123 pairs 49: Before cleaning: 123 dihedrals 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 6 donors and 4 acceptors were found. 49: There are 3 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 164 pairs 49: Before cleaning: 169 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 152 pairs 49: Before cleaning: 152 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 4 28 49: 49: 2 'B' 4 33 49: 49: 3 'B' 3 25 49: 49: 4 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (28 atoms, 4 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 4 residues with 51 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 50, now 50 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2 cmap torsion pairs 49: 49: There are 123 dihedrals, 9 impropers, 88 angles 49: 123 pairs, 50 bonds and 0 virtual sites 49: 49: Total mass 434.421 a.m.u. 49: 49: Total charge -2.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (33 atoms, 4 residues) 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: Start terminus PHE-6: NH3+ 49: End terminus ILE-9: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 4 residues with 66 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 67, now 67 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2 cmap torsion pairs 49: 49: There are 169 dihedrals, 13 impropers, 118 angles 49: 161 pairs, 67 bonds and 0 virtual sites 49: 49: Total mass 472.547 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'B' (25 atoms, 3 residues) 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 61 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 60, now 60 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 152 dihedrals, 5 impropers, 112 angles 49: 152 pairs, 60 bonds and 0 virtual sites 49: 49: Total mass 391.552 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Processing chain 4 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 51 atoms 4 residues 49: 49: Including chain 2 in system: 66 atoms 4 residues 49: 49: Including chain 3 in system: 61 atoms 3 residues 49: 49: Including chain 4 in system: 83 atoms 5 residues 49: 49: Now there are 261 atoms and 16 residues 49: 49: Total mass in system 1900.162 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (79 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 652 pairs 49: Before cleaning: 662 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records and chain id changing. 49: 49: Merged chains into joint molecule definitions at 1 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 256, now 256 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 12 cmap torsion pairs 49: 49: There are 662 dihedrals, 47 impropers, 460 angles 49: 649 pairs, 256 bonds and 0 virtual sites 49: 49: Total mass 1864.131 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (80 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 14 donors and 15 acceptors were found. 49: There are 20 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 441 pairs 49: Before cleaning: 446 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records and chain id changing. 49: 49: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 11 86 49: 49: 2 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (86 atoms, 11 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 11 residues with 172 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 173, now 173 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 9 cmap torsion pairs 49: 49: There are 446 dihedrals, 29 impropers, 312 angles 49: 438 pairs, 173 bonds and 0 virtual sites 49: 49: Total mass 1262.488 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 172 atoms 11 residues 49: 49: Including chain 2 in system: 83 atoms 5 residues 49: 49: Now there are 255 atoms and 16 residues 49: 49: Total mass in system 1864.131 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (68 ms) 49: [----------] 8 tests from ChainSep/Pdb2gmxTest (614 ms total) 49: 49: [----------] 4 tests from ChainChanges/Pdb2gmxTest 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on changing chain id only (ignoring TER records). 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (45 ms) 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records only (ignoring chain id). 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (45 ms) 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (43 ms) 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records and chain id changing. 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (45 ms) 49: [----------] 4 tests from ChainChanges/Pdb2gmxTest (181 ms total) 49: 49: [----------] 4 tests from Cyclic/Pdb2gmxTest 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: WARNING: all CONECT records are ignored 49: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 6040 pairs 49: Before cleaning: 6605 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 6040 pairs 49: Before cleaning: 6605 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 49: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: Moved all the water blocks to the end 49: 49: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 49: 49: chain #res #atoms 49: 49: 1 'P' 71 1527 49: 49: 2 'Q' 71 1527 49: 49: 3 'Q' 7 7 49: 49: 4 ' ' 10 10 (only water) 49: 49: 5 ' ' 16 16 (only water) 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'P' (1527 atoms, 71 residues) 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 71 residues with 2297 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 2481, now 2481 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 6605 dihedrals, 183 impropers, 4434 angles 49: 5827 pairs, 2481 bonds and 0 virtual sites 49: 49: Total mass 22984.514 a.m.u. 49: 49: Total charge -71.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'Q' (1527 atoms, 71 residues) 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 71 residues with 2297 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 2481, now 2481 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 6605 dihedrals, 183 impropers, 4434 angles 49: 5827 pairs, 2481 bonds and 0 virtual sites 49: 49: Total mass 22984.514 a.m.u. 49: 49: Total charge -71.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'Q' (7 atoms, 7 residues) 49: 49: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 49: 49: Disabling further notes about ions. 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 7 residues with 7 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: No bonds 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 0 angles 49: 0 pairs, 0 bonds and 0 virtual sites 49: 49: Total mass 170.135 a.m.u. 49: 49: Total charge 14.000 e 49: 49: Writing topology 49: 49: Processing chain 4 (10 atoms, 10 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 10 residues with 30 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 30, now 30 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 30 angles 49: 0 pairs, 30 bonds and 0 virtual sites 49: 49: Total mass 180.154 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Processing chain 5 (16 atoms, 16 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 48 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 48, now 48 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 48 angles 49: 0 pairs, 48 bonds and 0 virtual sites 49: 49: Total mass 288.246 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Including chain 1 in system: 2297 atoms 71 residues 49: 49: Including chain 2 in system: 2297 atoms 71 residues 49: 49: Including chain 3 in system: 7 atoms 7 residues 49: 49: Including chain 4 in system: 30 atoms 10 residues 49: 49: Including chain 5 in system: 48 atoms 16 residues 49: 49: Now there are 4679 atoms and 175 residues 49: 49: Total mass in system 46607.562 a.m.u. 49: 49: Total charge in system -128.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (3937 ms) 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 2325 pairs 49: Before cleaning: 2325 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 49: Read 'CARNOCYCLIN-A', 413 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 60 413 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (413 atoms, 60 residues) 49: 49: Identified residue LEU1 as a starting terminus. 49: 49: Identified residue LEU60 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 60 residues with 878 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 880, now 880 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 60 cmap torsion pairs 49: 49: There are 2325 dihedrals, 137 impropers, 1614 angles 49: 2319 pairs, 880 bonds and 0 virtual sites 49: 49: Total mass 5866.087 a.m.u. 49: 49: Total charge 4.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (624 ms) 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: WARNING: all CONECT records are ignored 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 12080 pairs 49: Before cleaning: 13210 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 49: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Moved all the water blocks to the end 49: 49: Merged chains into joint molecule definitions at 2 places. 49: 49: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 49: 49: chain #res #atoms 49: 49: 1 'P' 149 3061 49: 49: 2 ' ' 10 10 (only water) 49: 49: 3 ' ' 16 16 (only water) 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'P' (3061 atoms, 149 residues) 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 49: 49: Disabling further notes about ions. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 149 residues with 4601 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 4962, now 4962 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 13210 dihedrals, 366 impropers, 8868 angles 49: 11654 pairs, 4962 bonds and 0 virtual sites 49: 49: Total mass 46139.162 a.m.u. 49: 49: Total charge -128.000 e 49: 49: Writing topology 49: 49: Processing chain 2 (10 atoms, 10 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 10 residues with 30 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 30, now 30 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 30 angles 49: 0 pairs, 30 bonds and 0 virtual sites 49: 49: Total mass 180.154 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Processing chain 3 (16 atoms, 16 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 48 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 48, now 48 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 48 angles 49: 0 pairs, 48 bonds and 0 virtual sites 49: 49: Total mass 288.246 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Including chain 1 in system: 4601 atoms 149 residues 49: 49: Including chain 2 in system: 30 atoms 10 residues 49: 49: Including chain 3 in system: 48 atoms 16 residues 49: 49: Now there are 4679 atoms and 175 residues 49: 49: Total mass in system 46607.562 a.m.u. 49: 49: Total charge in system -128.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (6607 ms) 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 2325 pairs 49: Before cleaning: 2325 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 49: Read 'CARNOCYCLIN-A', 413 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 60 413 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (413 atoms, 60 residues) 49: 49: Identified residue LEU1 as a starting terminus. 49: 49: Identified residue LEU60 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 60 residues with 878 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 880, now 880 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 60 cmap torsion pairs 49: 49: There are 2325 dihedrals, 137 impropers, 1614 angles 49: 2319 pairs, 880 bonds and 0 virtual sites 49: 49: Total mass 5866.087 a.m.u. 49: 49: Total charge 4.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (302 ms) 49: [----------] 4 tests from Cyclic/Pdb2gmxTest (11472 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 39 tests from 6 test suites ran. (15516 ms total) 49: [ PASSED ] 39 tests. 49/81 Test #49: Pdb2gmx3Test ................................... Passed 15.58 sec test 50 Start 50: CorrelationsTest 50: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/CorrelationsTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/correlationfunctions/tests 50: Test timeout computed to be: 30 50: [==========] Running 21 tests from 3 test suites. 50: [----------] Global test environment set-up. 50: [----------] 10 tests from AutocorrTest 50: [ RUN ] AutocorrTest.EacNormal 50: [ OK ] AutocorrTest.EacNormal (134 ms) 50: [ RUN ] AutocorrTest.EacNoNormalize 50: [ OK ] AutocorrTest.EacNoNormalize (75 ms) 50: [ RUN ] AutocorrTest.EacCos 50: [ OK ] AutocorrTest.EacCos (127 ms) 50: [ RUN ] AutocorrTest.EacVector 50: [ OK ] AutocorrTest.EacVector (205 ms) 50: [ RUN ] AutocorrTest.EacRcross 50: [ OK ] AutocorrTest.EacRcross (1 ms) 50: [ RUN ] AutocorrTest.EacP0 50: [ OK ] AutocorrTest.EacP0 (224 ms) 50: [ RUN ] AutocorrTest.EacP1 50: [ OK ] AutocorrTest.EacP1 (195 ms) 50: [ RUN ] AutocorrTest.EacP2 50: [ OK ] AutocorrTest.EacP2 (387 ms) 50: [ RUN ] AutocorrTest.EacP3 50: [ OK ] AutocorrTest.EacP3 (4 ms) 50: [ RUN ] AutocorrTest.EacP4 50: [ OK ] AutocorrTest.EacP4 (195 ms) 50: [----------] 10 tests from AutocorrTest (1555 ms total) 50: 50: [----------] 10 tests from ExpfitTest 50: [ RUN ] ExpfitTest.EffnEXP1 50: [ OK ] ExpfitTest.EffnEXP1 (14 ms) 50: [ RUN ] ExpfitTest.EffnEXP2 50: [ OK ] ExpfitTest.EffnEXP2 (2 ms) 50: [ RUN ] ExpfitTest.EffnEXPEXP 50: [ OK ] ExpfitTest.EffnEXPEXP (1 ms) 50: [ RUN ] ExpfitTest.EffnEXP5 50: [ OK ] ExpfitTest.EffnEXP5 (16 ms) 50: [ RUN ] ExpfitTest.EffnEXP7 50: [ OK ] ExpfitTest.EffnEXP7 (8 ms) 50: [ RUN ] ExpfitTest.EffnEXP9 50: [ OK ] ExpfitTest.EffnEXP9 (75 ms) 50: [ RUN ] ExpfitTest.EffnERF 50: [ OK ] ExpfitTest.EffnERF (11 ms) 50: [ RUN ] ExpfitTest.EffnERREST 50: [ OK ] ExpfitTest.EffnERREST (7 ms) 50: [ RUN ] ExpfitTest.EffnVAC 50: [ OK ] ExpfitTest.EffnVAC (16 ms) 50: [ RUN ] ExpfitTest.EffnPRES 50: [ OK ] ExpfitTest.EffnPRES (49 ms) 50: [----------] 10 tests from ExpfitTest (203 ms total) 50: 50: [----------] 1 test from ManyAutocorrelationTest 50: [ RUN ] ManyAutocorrelationTest.Empty 50: [ OK ] ManyAutocorrelationTest.Empty (10 ms) 50: [----------] 1 test from ManyAutocorrelationTest (10 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 21 tests from 3 test suites ran. (1812 ms total) 50: [ PASSED ] 21 tests. 50/81 Test #50: CorrelationsTest ............................... Passed 1.85 sec test 51 Start 51: AnalysisDataUnitTests 51: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/analysisdata/tests 51: Test timeout computed to be: 30 51: [==========] Running 69 tests from 14 test suites. 51: [----------] Global test environment set-up. 51: [----------] 3 tests from AnalysisDataInitializationTest 51: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 51: [ OK ] AnalysisDataInitializationTest.BasicInitialization (8 ms) 51: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 51: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (16 ms) 51: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 51: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 51: [----------] 3 tests from AnalysisDataInitializationTest (24 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 51: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (16 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/0 (19 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 51: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/1 (8 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 51: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (6 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 51: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/2 (10 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 51: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (16 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/3 (20 ms total) 51: 51: [----------] 4 tests from AnalysisArrayDataTest 51: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 51: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (4 ms) 51: [ RUN ] AnalysisArrayDataTest.StorageWorks 51: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 51: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 51: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 51: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 51: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 51: [----------] 4 tests from AnalysisArrayDataTest (5 ms total) 51: 51: [----------] 6 tests from AverageModuleTest 51: [ RUN ] AverageModuleTest.BasicTest 51: [ OK ] AverageModuleTest.BasicTest (15 ms) 51: [ RUN ] AverageModuleTest.HandlesMultipointData 51: [ OK ] AverageModuleTest.HandlesMultipointData (8 ms) 51: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 51: [ OK ] AverageModuleTest.HandlesMultipleDataSets (1 ms) 51: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 51: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 51: [ RUN ] AverageModuleTest.CanCustomizeXAxis 51: [ OK ] AverageModuleTest.CanCustomizeXAxis (1 ms) 51: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 51: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 51: [----------] 6 tests from AverageModuleTest (28 ms total) 51: 51: [----------] 2 tests from FrameAverageModuleTest 51: [ RUN ] FrameAverageModuleTest.BasicTest 51: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 51: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 51: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (6 ms) 51: [----------] 2 tests from FrameAverageModuleTest (7 ms total) 51: 51: [----------] 7 tests from AnalysisHistogramSettingsTest 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 51: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 51: 51: [----------] 2 tests from SimpleHistogramModuleTest 51: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 51: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (2 ms) 51: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (5 ms) 51: [----------] 2 tests from SimpleHistogramModuleTest (8 ms total) 51: 51: [----------] 3 tests from WeightedHistogramModuleTest 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (7 ms) 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (8 ms) 51: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 51: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (1 ms) 51: [----------] 3 tests from WeightedHistogramModuleTest (17 ms total) 51: 51: [----------] 3 tests from BinAverageModuleTest 51: [ RUN ] BinAverageModuleTest.ComputesCorrectly 51: [ OK ] BinAverageModuleTest.ComputesCorrectly (1 ms) 51: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 51: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 51: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 51: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (1 ms) 51: [----------] 3 tests from BinAverageModuleTest (3 ms total) 51: 51: [----------] 4 tests from AbstractAverageHistogramTest 51: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 51: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (9 ms) 51: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 51: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (8 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (1 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (6 ms) 51: [----------] 4 tests from AbstractAverageHistogramTest (26 ms total) 51: 51: [----------] 3 tests from LifetimeModuleTest 51: [ RUN ] LifetimeModuleTest.BasicTest 51: [ OK ] LifetimeModuleTest.BasicTest (11 ms) 51: [ RUN ] LifetimeModuleTest.CumulativeTest 51: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 51: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 51: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 51: [----------] 3 tests from LifetimeModuleTest (13 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 69 tests from 14 test suites ran. (195 ms total) 51: [ PASSED ] 69 tests. 51/81 Test #51: AnalysisDataUnitTests .......................... Passed 0.25 sec test 52 Start 52: CoordinateIOTests 52: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/CoordinateIOTests.xml" 52: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/coordinateio/tests 52: Test timeout computed to be: 30 52: [==========] Running 64 tests from 19 test suites. 52: [----------] Global test environment set-up. 52: [----------] 1 test from OutputSelectorDeathTest 52: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (37 ms) 52: [----------] 1 test from OutputSelectorDeathTest (37 ms total) 52: 52: [----------] 5 tests from TrajectoryFrameWriterTest 52: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (27 ms) 52: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (4 ms) 52: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (12 ms) 52: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (31 ms) 52: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 52: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 52: [----------] 5 tests from TrajectoryFrameWriterTest (76 ms total) 52: 52: [----------] 5 tests from OutputAdapterContainer 52: [ RUN ] OutputAdapterContainer.MakeEmpty 52: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 52: [ RUN ] OutputAdapterContainer.AddAdapter 52: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 52: [ RUN ] OutputAdapterContainer.RejectBadAdapter 52: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 52: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 52: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (6 ms) 52: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 52: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 52: [----------] 5 tests from OutputAdapterContainer (7 ms total) 52: 52: [----------] 5 tests from FlagTest 52: [ RUN ] FlagTest.CanSetSimpleFlag 52: [ OK ] FlagTest.CanSetSimpleFlag (7 ms) 52: [ RUN ] FlagTest.CanAddNewBox 52: [ OK ] FlagTest.CanAddNewBox (0 ms) 52: [ RUN ] FlagTest.SetsImplicitPrecisionChange 52: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 52: [ RUN ] FlagTest.SetsImplicitStartTimeChange 52: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 52: [ RUN ] FlagTest.SetsImplicitTimeStepChange 52: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 52: [----------] 5 tests from FlagTest (8 ms total) 52: 52: [----------] 5 tests from SetAtomsTest 52: [ RUN ] SetAtomsTest.RemovesExistingAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.RemovesExistingAtoms (4 ms) 52: [ RUN ] SetAtomsTest.AddsNewAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.AddsNewAtoms (12 ms) 52: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (12 ms) 52: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (4 ms) 52: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (12 ms) 52: [----------] 5 tests from SetAtomsTest (47 ms total) 52: 52: [----------] 2 tests from SetBothTimeTest 52: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 52: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 52: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 52: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 52: [----------] 2 tests from SetBothTimeTest (0 ms total) 52: 52: [----------] 2 tests from SetStartTimeTest 52: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 52: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (4 ms) 52: [ RUN ] SetStartTimeTest.WorksWithZeroStart 52: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 52: [----------] 2 tests from SetStartTimeTest (4 ms total) 52: 52: [----------] 1 test from SetTimeStepTest 52: [ RUN ] SetTimeStepTest.SetTimeStepWorks 52: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 52: [----------] 1 test from SetTimeStepTest (0 ms total) 52: 52: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (14 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (4 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (12 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (8 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (12 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (12 ms) 52: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (64 ms total) 52: 52: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 52: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (8 ms) 52: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (12 ms) 52: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (4 ms) 52: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (25 ms total) 52: 52: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 52: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 52: 52: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (20 ms) 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (25 ms) 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (23 ms) 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (22 ms) 52: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (91 ms total) 52: 52: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 52: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (4 ms) 52: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (4 ms) 52: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (6 ms) 52: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (15 ms total) 52: 52: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 52: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 52: 52: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 52: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (4 ms) 52: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (6 ms) 52: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (10 ms total) 52: 52: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 52: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 52: 52: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 52: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (9 ms) 52: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (4 ms) 52: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (13 ms total) 52: 52: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 52: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 52: 52: [----------] 4 tests from ModuleSupported/NoOptionalOutput 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (4 ms) 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (4 ms) 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (4 ms) 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (4 ms) 52: [----------] 4 tests from ModuleSupported/NoOptionalOutput (17 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 64 tests from 19 test suites ran. (421 ms total) 52: [ PASSED ] 64 tests. 52/81 Test #52: CoordinateIOTests .............................. Passed 0.48 sec test 53 Start 53: TrajectoryAnalysisUnitTests 53: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests 53: Test timeout computed to be: 1920 53: [==========] Running 96 tests from 17 test suites. 53: [----------] Global test environment set-up. 53: [----------] 11 tests from AngleModuleTest 53: [ RUN ] AngleModuleTest.ComputesSimpleAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesSimpleAngles (39 ms) 53: [ RUN ] AngleModuleTest.ComputesDihedrals 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesDihedrals (8 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorPairAngles (8 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (12 ms) 53: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (15 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (12 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 53: Reading frames from gro file 'Test system for different angles', 33 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (8 ms) 53: [ RUN ] AngleModuleTest.ComputesMultipleAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesMultipleAngles (12 ms) 53: [ RUN ] AngleModuleTest.HandlesDynamicSelections 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.HandlesDynamicSelections (11 ms) 53: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (12 ms) 53: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (4 ms) 53: [----------] 11 tests from AngleModuleTest (144 ms total) 53: 53: [----------] 5 tests from ClustsizeTest 53: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 53: There is one group in the index 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 24 53: cmid: 2, cmax: 4, max_size: 6 53: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 53: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (12 ms) 53: [ RUN ] ClustsizeTest.NoMolShortCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 53: There is one group in the index 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 24 53: cmid: 1, cmax: 6, max_size: 6 53: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 53: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (5 ms) 53: [ RUN ] ClustsizeTest.MolDefaultCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 8 53: cmid: 2, cmax: 4, max_size: 2 53: 50%100%cmid: 2, cmax: 6, max_size: 2 53: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (4 ms) 53: [ RUN ] ClustsizeTest.MolShortCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 8 53: cmid: 1, cmax: 6, max_size: 2 53: 50%100%cmid: 2, cmax: 6, max_size: 2 53: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (3 ms) 53: [ RUN ] ClustsizeTest.MolCSize 53: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 8 53: cmid: 2, cmax: 4, max_size: 2 53: 50%100%cmid: 2, cmax: 6, max_size: 2 53: 50%100%[ OK ] ClustsizeTest.MolCSize (8 ms) 53: [----------] 5 tests from ClustsizeTest (33 ms total) 53: 53: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 53: Reading frames from gro file 'Test system', 8 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (11 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 53: Reading frames from gro file 'Test system', 8 atoms. 53: Reading frame 0 time 0.000 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (21 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 53: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (34 ms total) 53: 53: [----------] 4 tests from ConvertTrjModuleTest 53: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (52 ms) 53: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (25 ms) 53: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (6 ms) 53: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (3 ms) 53: [----------] 4 tests from ConvertTrjModuleTest (89 ms total) 53: 53: [----------] 6 tests from DistanceModuleTest 53: [ RUN ] DistanceModuleTest.ComputesDistances 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: atomname S1 S2: 53: Number of samples: 5 53: Average distance: 1.43246 nm 53: Standard deviation: 0.96700 nm 53: [ OK ] DistanceModuleTest.ComputesDistances (14 ms) 53: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: atomname S1 S2: 53: Number of samples: 5 53: Average distance: 1.43246 nm 53: Standard deviation: 0.96700 nm 53: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 53: Number of samples: 4 53: Average distance: 1.81066 nm 53: Standard deviation: 0.79289 nm 53: [ OK ] DistanceModuleTest.ComputesMultipleDistances (12 ms) 53: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: atomname S1 S2 and res_cog x < 2.8: 53: Number of samples: 3 53: Average distance: 1.72076 nm 53: Standard deviation: 1.24839 nm 53: [ OK ] DistanceModuleTest.HandlesDynamicSelections (15 ms) 53: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: Contacts: 53: Number of samples: 2 53: Average distance: 1.00000 nm 53: Standard deviation: 0.00000 nm 53: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (51 ms) 53: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: SuccessiveContacts: 53: Number of samples: 2 53: Average distance: 1.00000 nm 53: Standard deviation: 0.00000 nm 53: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (34 ms) 53: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: ManyContacts: 53: Number of samples: 10 53: Average distance: 1.82913 nm 53: Standard deviation: 0.78478 nm 53: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (39 ms) 53: [----------] 6 tests from DistanceModuleTest (172 ms total) 53: 53: [----------] 2 tests from ExtractClusterModuleTest 53: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 53: trr version: GMX_trn_file (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 53: Analyzed 26 frames, last time 0.050 53: There are 8 clusters containing 26 structures, highest framenr is 25 53: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (11 ms) 53: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 53: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 53: Analyzed 26 frames, last time 0.050 53: There are 8 clusters containing 26 structures, highest framenr is 25 53: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (5 ms) 53: [----------] 2 tests from ExtractClusterModuleTest (16 ms total) 53: 53: [----------] 2 tests from FreeVolumeModuleTest 53: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for 40 particles. These were set to zero. 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: cutoff = 0.18 nm 53: probe_radius = 0 nm 53: seed = 13 53: ninsert = 1000 probes per nm^3 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 53: van der Spoel and Luciano T. Costa 53: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 53: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 53: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Free volume 38.02 +/- 0.00 % 53: Total volume 68.92 +/- 0.00 nm^3 53: Number of molecules 340 total mass 63491.38 Dalton 53: Average molar mass: 186.74 Dalton 53: Density rho: 1529.71 +/- 0.00 nm^3 53: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 53: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 53: Fractional free volume 0.194 +/- 0.000 53: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (272 ms) 53: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: cutoff = 0.18 nm 53: probe_radius = 0 nm 53: seed = 17 53: ninsert = 1000 probes per nm^3 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 53: van der Spoel and Luciano T. Costa 53: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 53: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 53: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Free volume 38.48 +/- 0.00 % 53: Total volume 68.92 +/- 0.00 nm^3 53: Number of molecules 340 total mass 63491.38 Dalton 53: Average molar mass: 186.74 Dalton 53: Density rho: 1529.71 +/- 0.00 nm^3 53: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 53: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 53: Fractional free volume 0.200 +/- 0.000 53: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (268 ms) 53: [----------] 2 tests from FreeVolumeModuleTest (540 ms total) 53: 53: [----------] 11 tests from MsdModuleTest 53: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.threeDimensionalDiffusion (23 ms) 53: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.twoDimensionalDiffusion (3 ms) 53: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.oneDimensionalDiffusion (7 ms) 53: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (11 ms) 53: [ RUN ] MsdModuleTest.multipleGroupsWork 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to 1576763263 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.multipleGroupsWork (126 ms) 53: [ RUN ] MsdModuleTest.trestartLessThanDt 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to 1057995737 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.trestartLessThanDt (77 ms) 53: [ RUN ] MsdModuleTest.trestartGreaterThanDt 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -881008641 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.trestartGreaterThanDt (81 ms) 53: [ RUN ] MsdModuleTest.molTest 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to 952855031 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.molTest (60 ms) 53: [ RUN ] MsdModuleTest.beginFit 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to 2145348982 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.beginFit (50 ms) 53: [ RUN ] MsdModuleTest.endFit 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -302389297 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.endFit (45 ms) 53: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: NOTE: You provided an index file 53: /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 53: (with -n), but it was not used by any selection. 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -417793 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (41 ms) 53: [----------] 11 tests from MsdModuleTest (530 ms total) 53: 53: [----------] 9 tests from PairDistanceModuleTest 53: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesAllDistances (5 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (4 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (4 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (4 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (4 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (4 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (5 ms) 53: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (4 ms) 53: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (4 ms) 53: [----------] 9 tests from PairDistanceModuleTest (42 ms total) 53: 53: [----------] 5 tests from RdfModuleTest 53: [ RUN ] RdfModuleTest.BasicTest 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.BasicTest (43 ms) 53: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 53: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (24 ms) 53: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (37 ms) 53: [ RUN ] RdfModuleTest.CalculatesSurf 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.CalculatesSurf (25 ms) 53: [ RUN ] RdfModuleTest.CalculatesXY 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.CalculatesXY (40 ms) 53: [----------] 5 tests from RdfModuleTest (170 ms total) 53: 53: [----------] 5 tests from SasaModuleTest 53: [ RUN ] SasaModuleTest.BasicTest 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.BasicTest (34 ms) 53: [ RUN ] SasaModuleTest.HandlesSelectedResidues 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.HandlesSelectedResidues (13 ms) 53: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (11 ms) 53: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (14 ms) 53: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (42 ms) 53: [----------] 5 tests from SasaModuleTest (120 ms total) 53: 53: [----------] 8 tests from SelectModuleTest 53: [ RUN ] SelectModuleTest.BasicTest 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.BasicTest (20 ms) 53: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (14 ms) 53: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (8 ms) 53: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (15 ms) 53: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (4 ms) 53: [ RUN ] SelectModuleTest.NormalizesSizes 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.NormalizesSizes (9 ms) 53: [ RUN ] SelectModuleTest.WritesResidueNumbers 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.WritesResidueNumbers (17 ms) 53: [ RUN ] SelectModuleTest.WritesResidueIndices 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.WritesResidueIndices (5 ms) 53: [----------] 8 tests from SelectModuleTest (97 ms total) 53: 53: [----------] 10 tests from SurfaceAreaTest 53: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 53: [ OK ] SurfaceAreaTest.ComputesSinglePoint (5 ms) 53: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 53: [ OK ] SurfaceAreaTest.ComputesTwoPoints (2 ms) 53: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 53: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (1 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints12 53: [ OK ] SurfaceAreaTest.SurfacePoints12 (4 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints32 53: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints42 53: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints122 53: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms) 53: [ RUN ] SurfaceAreaTest.Computes100Points 53: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (7 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (12 ms) 53: [----------] 10 tests from SurfaceAreaTest (37 ms total) 53: 53: [----------] 4 tests from TopologyInformation 53: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 53: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 53: [ RUN ] TopologyInformation.WorksWithGroFile 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TopologyInformation.WorksWithGroFile (9 ms) 53: [ RUN ] TopologyInformation.WorksWithPdbFile 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TopologyInformation.WorksWithPdbFile (16 ms) 53: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file lysozyme.top, line 1465]: 53: System has non-zero total charge: 2.000000 53: Total charge should normally be an integer. See 53: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 53: for discussion on how close it should be to an integer. 53: 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 465.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 53: NVE simulation with an initial temperature of zero: will use a Verlet 53: buffer of 10%. Check your energy drift! 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Setting the LD random seed to -2695553 53: 53: Generated 330891 of the 330891 non-bonded parameter combinations 53: 53: Generated 330891 of the 330891 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 53: Analysing residue names: 53: There are: 10 Protein residues 53: Analysing Protein... 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (1117 ms) 53: [----------] 4 tests from TopologyInformation (1144 ms total) 53: 53: [----------] 4 tests from TrajectoryModuleTest 53: [ RUN ] TrajectoryModuleTest.BasicTest 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.BasicTest (12 ms) 53: [ RUN ] TrajectoryModuleTest.PlotsXOnly 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.PlotsXOnly (8 ms) 53: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (12 ms) 53: [ RUN ] TrajectoryModuleTest.HandlesNoForces 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.HandlesNoForces (4 ms) 53: [----------] 4 tests from TrajectoryModuleTest (41 ms total) 53: 53: [----------] 5 tests from UnionFinderTest 53: [ RUN ] UnionFinderTest.WorksEmpty 53: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 53: [ RUN ] UnionFinderTest.BasicMerges 53: [ OK ] UnionFinderTest.BasicMerges (0 ms) 53: [ RUN ] UnionFinderTest.LargerMerges 53: [ OK ] UnionFinderTest.LargerMerges (0 ms) 53: [ RUN ] UnionFinderTest.LongRightMerge 53: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 53: [ RUN ] UnionFinderTest.LongLeftMerge 53: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 53: [----------] 5 tests from UnionFinderTest (0 ms total) 53: 53: [----------] 1 test from MappedUnionFinderTest 53: [ RUN ] MappedUnionFinderTest.BasicMerges 53: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 53: [----------] 1 test from MappedUnionFinderTest (0 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 96 tests from 17 test suites ran. (3218 ms total) 53: [ PASSED ] 96 tests. 53/81 Test #53: TrajectoryAnalysisUnitTests .................... Passed 3.29 sec test 54 Start 54: EnergyAnalysisUnitTests 54: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/energyanalysis/tests 54: Test timeout computed to be: 30 54: [==========] Running 7 tests from 4 test suites. 54: [----------] Global test environment set-up. 54: [----------] 1 test from DhdlTest 54: [ RUN ] DhdlTest.ExtractDhdl 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 54: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 54: Note: file tpx version 110, software tpx version 127 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 54: 54: 54: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 54: [ OK ] DhdlTest.ExtractDhdl (65 ms) 54: [----------] 1 test from DhdlTest (65 ms total) 54: 54: [----------] 1 test from OriresTest 54: [ RUN ] OriresTest.ExtractOrires 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 54: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 54: Note: file tpx version 111, software tpx version 127 54: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 54: End your selection with 0 54: Selecting all 7 orientation restraints 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 54: [ OK ] OriresTest.ExtractOrires (112 ms) 54: [----------] 1 test from OriresTest (112 ms total) 54: 54: [----------] 3 tests from EnergyTest 54: [ RUN ] EnergyTest.ExtractEnergy 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: 54: Select the terms you want from the following list by 54: selecting either (part of) the name or the number or a combination. 54: End your selection with an empty line or a zero. 54: ------------------------------------------------------------------- 54: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 54: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 54: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 54: 13 Box-Z 14 Volume 15 Density 16 pV 54: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 54: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 54: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 54: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 54: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 54: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 54: 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 54: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 54: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 54: [ OK ] EnergyTest.ExtractEnergy (7 ms) 54: [ RUN ] EnergyTest.ExtractEnergyByNumber 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: 54: Select the terms you want from the following list by 54: selecting either (part of) the name or the number or a combination. 54: End your selection with an empty line or a zero. 54: ------------------------------------------------------------------- 54: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 54: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 54: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 54: 13 Box-Z 14 Volume 15 Density 16 pV 54: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 54: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 54: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 54: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 54: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 54: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 54: 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 54: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 54: Pres. DC -268.49 3 8.52175 13.2804 (bar) 54: [ OK ] EnergyTest.ExtractEnergyByNumber (3 ms) 54: [ RUN ] EnergyTest.ExtractEnergyMixed 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: 54: Select the terms you want from the following list by 54: selecting either (part of) the name or the number or a combination. 54: End your selection with an empty line or a zero. 54: ------------------------------------------------------------------- 54: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 54: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 54: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 54: 13 Box-Z 14 Volume 15 Density 16 pV 54: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 54: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 54: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 54: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 54: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 54: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 54: 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 54: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 54: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 54: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 54: [ OK ] EnergyTest.ExtractEnergyMixed (11 ms) 54: [----------] 3 tests from EnergyTest (23 ms total) 54: 54: [----------] 2 tests from ViscosityTest 54: [ RUN ] ViscosityTest.EinsteinViscosity 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Pres-XX 20.2092 65 717.193 185.978 (bar) 54: Pres-XY -47.7351 39 372.522 207.456 (bar) 54: Pres-XZ 11.477 31 379.79 6.80818 (bar) 54: Pres-YX -47.7106 39 372.525 207.5 (bar) 54: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 54: Pres-YZ -41.3534 45 401.216 114.663 (bar) 54: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 54: Pres-ZY -41.3119 45 401.196 114.743 (bar) 54: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 54: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 54: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 54: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 54: [ OK ] ViscosityTest.EinsteinViscosity (255 ms) 54: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Pres-XX 20.2092 65 717.193 185.978 (bar) 54: Pres-XY -47.7351 39 372.522 207.456 (bar) 54: Pres-XZ 11.477 31 379.79 6.80818 (bar) 54: Pres-YX -47.7106 39 372.525 207.5 (bar) 54: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 54: Pres-YZ -41.3534 45 401.216 114.663 (bar) 54: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 54: Pres-ZY -41.3119 45 401.196 114.743 (bar) 54: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 54: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 54: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 54: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 54: [ OK ] ViscosityTest.EinsteinViscosityIntegral (251 ms) 54: [----------] 2 tests from ViscosityTest (507 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 7 tests from 4 test suites ran. (709 ms total) 54: [ PASSED ] 7 tests. 54/81 Test #54: EnergyAnalysisUnitTests ........................ Passed 0.77 sec test 55 Start 55: ToolUnitTests 55: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/ToolUnitTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests 55: Test timeout computed to be: 1920 55: [==========] Running 54 tests from 6 test suites. 55: [----------] Global test environment set-up. 55: [----------] 2 tests from DumpTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Setting the LD random seed to -807717407 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: [ RUN ] DumpTest.WorksWithTpr 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 55: inputrec: 55: integrator = md 55: tinit = 0 55: dt = 0.001 55: nsteps = 0 55: init-step = 0 55: simulation-part = 1 55: mts = false 55: comm-mode = Linear 55: nstcomm = 100 55: bd-fric = 0 55: ld-seed = -807717407 55: emtol = 10 55: emstep = 0.01 55: niter = 20 55: fcstep = 0 55: nstcgsteep = 1000 55: nbfgscorr = 10 55: rtpi = 0.05 55: nstxout = 0 55: nstvout = 0 55: nstfout = 0 55: nstlog = 1000 55: nstcalcenergy = 100 55: nstenergy = 1000 55: nstxout-compressed = 0 55: compressed-x-precision = 1000 55: cutoff-scheme = Verlet 55: nstlist = 10 55: pbc = xyz 55: periodic-molecules = false 55: verlet-buffer-tolerance = -1 55: rlist = 1.1 55: coulombtype = Cut-off 55: coulomb-modifier = Potential-shift 55: rcoulomb-switch = 0 55: rcoulomb = 1 55: epsilon-r = 1 55: epsilon-rf = inf 55: vdw-type = Cut-off 55: vdw-modifier = Potential-shift 55: rvdw-switch = 0 55: rvdw = 1 55: DispCorr = No 55: table-extension = 1 55: fourierspacing = 0.12 55: fourier-nx = 0 55: fourier-ny = 0 55: fourier-nz = 0 55: pme-order = 4 55: ewald-rtol = 1e-05 55: ewald-rtol-lj = 0.001 55: lj-pme-comb-rule = Geometric 55: ewald-geometry = 3d 55: epsilon-surface = 0 55: tcoupl = No 55: nsttcouple = -1 55: nh-chain-length = 0 55: print-nose-hoover-chain-variables = false 55: pcoupl = No 55: pcoupltype = Isotropic 55: nstpcouple = -1 55: tau-p = 1 55: compressibility (3x3): 55: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: ref-p (3x3): 55: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: refcoord-scaling = No 55: posres-com (3): 55: posres-com[0]= 0.00000e+00 55: posres-com[1]= 0.00000e+00 55: posres-com[2]= 0.00000e+00 55: posres-comB (3): 55: posres-comB[0]= 0.00000e+00 55: posres-comB[1]= 0.00000e+00 55: posres-comB[2]= 0.00000e+00 55: QMMM = false 55: qm-opts: 55: ngQM = 0 55: constraint-algorithm = Lincs 55: continuation = false 55: Shake-SOR = false 55: shake-tol = 0.0001 55: lincs-order = 4 55: lincs-iter = 1 55: lincs-warnangle = 30 55: nwall = 0 55: wall-type = 9-3 55: wall-r-linpot = -1 55: wall-atomtype[0] = -1 55: wall-atomtype[1] = -1 55: wall-density[0] = 0 55: wall-density[1] = 0 55: wall-ewald-zfac = 3 55: pull = false 55: awh = false 55: rotation = false 55: interactiveMD = false 55: disre = No 55: disre-weighting = Conservative 55: disre-mixed = false 55: dr-fc = 1000 55: dr-tau = 0 55: nstdisreout = 100 55: orire-fc = 0 55: orire-tau = 0 55: nstorireout = 100 55: free-energy = no 55: cos-acceleration = 0 55: deform (3x3): 55: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: simulated-tempering = false 55: swapcoords = no 55: userint1 = 0 55: userint2 = 0 55: userint3 = 0 55: userint4 = 0 55: userreal1 = 0 55: userreal2 = 0 55: userreal3 = 0 55: userreal4 = 0 55: applied-forces: 55: electric-field: 55: x: 55: E0 = 0 55: omega = 0 55: t0 = 0 55: sigma = 0 55: y: 55: E0 = 0 55: omega = 0 55: t0 = 0 55: sigma = 0 55: z: 55: E0 = 0 55: omega = 0 55: t0 = 0 55: sigma = 0 55: density-guided-simulation: 55: active = false 55: group = protein 55: similarity-measure = inner-product 55: atom-spreading-weight = unity 55: force-constant = 1e+09 55: gaussian-transform-spreading-width = 0.2 55: gaussian-transform-spreading-range-in-multiples-of-width = 4 55: reference-density-filename = reference.mrc 55: nst = 1 55: normalize-densities = true 55: adaptive-force-scaling = false 55: adaptive-force-scaling-time-constant = 4 55: shift-vector = 55: transformation-matrix = 55: qmmm-cp2k: 55: active = false 55: qmgroup = System 55: qmmethod = PBE 55: qmfilenames = 55: qmcharge = 0 55: qmmultiplicity = 1 55: grpopts: 55: nrdf: 465 55: ref-t: 0 55: tau-t: 0 55: annealing: No 55: annealing-npoints: 0 55: acc: 0 0 0 55: nfreeze: N N N 55: energygrp-flags[ 0]: 0 55: header: 55: bIr = present 55: bBox = present 55: bTop = present 55: bX = present 55: bV = present 55: bF = not present 55: natoms = 156 55: lambda = 0.000000e+00 55: buffer size = 59646 55: topology: 55: name="First 10 residues from 1AKI" 55: #atoms = 156 55: #molblock = 1 55: molblock (0): 55: moltype = 0 "Protein_chain_B" 55: #molecules = 1 55: #posres_xA = 0 55: #posres_xB = 0 55: bIntermolecularInteractions = false 55: ffparams: 55: atnr=10 55: ntypes=212 55: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 55: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 55: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 55: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 55: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 55: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 55: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 55: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 55: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 55: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 55: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 55: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 55: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 55: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 55: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 55: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 55: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 55: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 55: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 55: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 55: functype[33]=LJ_SR, c6= 1.22578131e-04, 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functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 55: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 55: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 55: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 55: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 55: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 55: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 55: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 55: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 55: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 55: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 55: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 55: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 55: functype[64]=LJ_SR, c6= 3.38512054e-03, 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functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 55: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 55: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 55: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 55: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 55: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 55: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 55: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 55: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 55: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 55: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 55: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 55: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 55: functype[95]=LJ_SR, c6= 6.04976481e-03, 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2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 55: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 55: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 55: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 55: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 55: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 55: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 55: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 55: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 55: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 55: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 55: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 55: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 55: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 55: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 55: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 55: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 55: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 55: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 55: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 55: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 55: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 55: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 55: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 55: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 55: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 55: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 55: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 55: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 55: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 55: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 55: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 55: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 55: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 55: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 55: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 55: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 55: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 55: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 55: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 55: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 55: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 55: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 55: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 55: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 55: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 55: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 55: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 55: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 55: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 55: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 55: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 55: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 55: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 55: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 55: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 55: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 55: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 55: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 55: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 55: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 55: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 55: reppow = 12 55: fudgeQQ = 0.5 55: cmap 55: atomtypes: 55: atomtype[ 0]={atomnumber= 7} 55: atomtype[ 1]={atomnumber= 1} 55: atomtype[ 2]={atomnumber= 6} 55: atomtype[ 3]={atomnumber= 1} 55: atomtype[ 4]={atomnumber= 6} 55: atomtype[ 5]={atomnumber= 8} 55: atomtype[ 6]={atomnumber= 6} 55: atomtype[ 7]={atomnumber= 1} 55: atomtype[ 8]={atomnumber= 6} 55: atomtype[ 9]={atomnumber= 16} 55: moltype (0): 55: name="Protein_chain_B" 55: atoms: 55: atom (156): 55: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 55: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 55: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 55: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 55: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 55: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 55: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 55: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 55: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 55: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 55: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 55: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 55: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 55: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 55: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 55: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 55: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 55: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 55: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 55: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 55: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 55: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 55: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 55: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 55: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 55: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 55: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 55: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 55: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 55: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 55: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 55: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 55: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 55: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 55: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 55: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 55: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 55: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 55: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 55: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 55: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 55: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 55: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 55: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 55: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 55: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 55: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 55: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 55: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 55: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 55: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 55: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 55: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 55: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 55: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 55: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 55: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 55: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 55: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 55: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 55: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 55: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 55: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 55: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 55: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 55: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 55: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 55: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 55: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 55: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 55: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 55: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 55: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 55: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 55: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 55: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 55: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 55: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 55: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 55: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 55: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 55: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 55: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 55: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 55: atom (156): 55: atom[0]={name="N"} 55: atom[1]={name="H1"} 55: atom[2]={name="H2"} 55: atom[3]={name="H3"} 55: atom[4]={name="CA"} 55: atom[5]={name="HA"} 55: atom[6]={name="CB"} 55: atom[7]={name="HB1"} 55: atom[8]={name="HB2"} 55: atom[9]={name="CG"} 55: atom[10]={name="HG1"} 55: atom[11]={name="HG2"} 55: atom[12]={name="CD"} 55: atom[13]={name="HD1"} 55: atom[14]={name="HD2"} 55: atom[15]={name="CE"} 55: atom[16]={name="HE1"} 55: atom[17]={name="HE2"} 55: atom[18]={name="NZ"} 55: atom[19]={name="HZ1"} 55: atom[20]={name="HZ2"} 55: atom[21]={name="HZ3"} 55: atom[22]={name="C"} 55: atom[23]={name="O"} 55: atom[24]={name="N"} 55: atom[25]={name="H"} 55: atom[26]={name="CA"} 55: atom[27]={name="HA"} 55: atom[28]={name="CB"} 55: atom[29]={name="HB"} 55: atom[30]={name="CG1"} 55: atom[31]={name="HG11"} 55: atom[32]={name="HG12"} 55: atom[33]={name="HG13"} 55: atom[34]={name="CG2"} 55: atom[35]={name="HG21"} 55: atom[36]={name="HG22"} 55: atom[37]={name="HG23"} 55: atom[38]={name="C"} 55: atom[39]={name="O"} 55: atom[40]={name="N"} 55: atom[41]={name="H"} 55: atom[42]={name="CA"} 55: atom[43]={name="HA"} 55: atom[44]={name="CB"} 55: atom[45]={name="HB1"} 55: atom[46]={name="HB2"} 55: atom[47]={name="CG"} 55: atom[48]={name="CD1"} 55: atom[49]={name="HD1"} 55: atom[50]={name="CD2"} 55: atom[51]={name="HD2"} 55: atom[52]={name="CE1"} 55: atom[53]={name="HE1"} 55: atom[54]={name="CE2"} 55: atom[55]={name="HE2"} 55: atom[56]={name="CZ"} 55: atom[57]={name="HZ"} 55: atom[58]={name="C"} 55: atom[59]={name="O"} 55: atom[60]={name="N"} 55: atom[61]={name="H"} 55: atom[62]={name="CA"} 55: atom[63]={name="HA1"} 55: atom[64]={name="HA2"} 55: atom[65]={name="C"} 55: atom[66]={name="O"} 55: atom[67]={name="N"} 55: atom[68]={name="H"} 55: atom[69]={name="CA"} 55: atom[70]={name="HA"} 55: atom[71]={name="CB"} 55: atom[72]={name="HB1"} 55: atom[73]={name="HB2"} 55: atom[74]={name="CG"} 55: atom[75]={name="HG1"} 55: atom[76]={name="HG2"} 55: atom[77]={name="CD"} 55: atom[78]={name="HD1"} 55: atom[79]={name="HD2"} 55: atom[80]={name="NE"} 55: atom[81]={name="HE"} 55: atom[82]={name="CZ"} 55: atom[83]={name="NH1"} 55: atom[84]={name="HH11"} 55: atom[85]={name="HH12"} 55: atom[86]={name="NH2"} 55: atom[87]={name="HH21"} 55: atom[88]={name="HH22"} 55: atom[89]={name="C"} 55: atom[90]={name="O"} 55: atom[91]={name="N"} 55: atom[92]={name="H"} 55: atom[93]={name="CA"} 55: atom[94]={name="HA"} 55: atom[95]={name="CB"} 55: atom[96]={name="HB1"} 55: atom[97]={name="HB2"} 55: atom[98]={name="SG"} 55: atom[99]={name="HG"} 55: atom[100]={name="C"} 55: atom[101]={name="O"} 55: atom[102]={name="N"} 55: atom[103]={name="H"} 55: atom[104]={name="CA"} 55: atom[105]={name="HA"} 55: atom[106]={name="CB"} 55: atom[107]={name="HB1"} 55: atom[108]={name="HB2"} 55: atom[109]={name="CG"} 55: atom[110]={name="HG1"} 55: atom[111]={name="HG2"} 55: atom[112]={name="CD"} 55: atom[113]={name="OE1"} 55: atom[114]={name="OE2"} 55: atom[115]={name="C"} 55: atom[116]={name="O"} 55: atom[117]={name="N"} 55: atom[118]={name="H"} 55: atom[119]={name="CA"} 55: atom[120]={name="HA"} 55: atom[121]={name="CB"} 55: atom[122]={name="HB1"} 55: atom[123]={name="HB2"} 55: atom[124]={name="CG"} 55: atom[125]={name="HG"} 55: atom[126]={name="CD1"} 55: atom[127]={name="HD11"} 55: atom[128]={name="HD12"} 55: atom[129]={name="HD13"} 55: atom[130]={name="CD2"} 55: atom[131]={name="HD21"} 55: atom[132]={name="HD22"} 55: atom[133]={name="HD23"} 55: atom[134]={name="C"} 55: atom[135]={name="O"} 55: atom[136]={name="N"} 55: atom[137]={name="H"} 55: atom[138]={name="CA"} 55: atom[139]={name="HA"} 55: atom[140]={name="CB"} 55: atom[141]={name="HB1"} 55: atom[142]={name="HB2"} 55: atom[143]={name="HB3"} 55: atom[144]={name="C"} 55: atom[145]={name="O"} 55: atom[146]={name="N"} 55: atom[147]={name="H"} 55: atom[148]={name="CA"} 55: atom[149]={name="HA"} 55: atom[150]={name="CB"} 55: atom[151]={name="HB1"} 55: atom[152]={name="HB2"} 55: atom[153]={name="HB3"} 55: atom[154]={name="C"} 55: atom[155]={name="O"} 55: type (156): 55: type[0]={name="opls_287",nameB="opls_287"} 55: type[1]={name="opls_290",nameB="opls_290"} 55: type[2]={name="opls_290",nameB="opls_290"} 55: type[3]={name="opls_290",nameB="opls_290"} 55: type[4]={name="opls_293B",nameB="opls_293B"} 55: type[5]={name="opls_140",nameB="opls_140"} 55: type[6]={name="opls_136",nameB="opls_136"} 55: type[7]={name="opls_140",nameB="opls_140"} 55: type[8]={name="opls_140",nameB="opls_140"} 55: type[9]={name="opls_136",nameB="opls_136"} 55: type[10]={name="opls_140",nameB="opls_140"} 55: type[11]={name="opls_140",nameB="opls_140"} 55: type[12]={name="opls_136",nameB="opls_136"} 55: type[13]={name="opls_140",nameB="opls_140"} 55: type[14]={name="opls_140",nameB="opls_140"} 55: type[15]={name="opls_292",nameB="opls_292"} 55: type[16]={name="opls_140",nameB="opls_140"} 55: type[17]={name="opls_140",nameB="opls_140"} 55: type[18]={name="opls_287",nameB="opls_287"} 55: type[19]={name="opls_290",nameB="opls_290"} 55: type[20]={name="opls_290",nameB="opls_290"} 55: type[21]={name="opls_290",nameB="opls_290"} 55: type[22]={name="opls_235",nameB="opls_235"} 55: type[23]={name="opls_236",nameB="opls_236"} 55: type[24]={name="opls_238",nameB="opls_238"} 55: type[25]={name="opls_241",nameB="opls_241"} 55: type[26]={name="opls_224B",nameB="opls_224B"} 55: type[27]={name="opls_140",nameB="opls_140"} 55: type[28]={name="opls_137",nameB="opls_137"} 55: type[29]={name="opls_140",nameB="opls_140"} 55: type[30]={name="opls_135",nameB="opls_135"} 55: type[31]={name="opls_140",nameB="opls_140"} 55: type[32]={name="opls_140",nameB="opls_140"} 55: type[33]={name="opls_140",nameB="opls_140"} 55: type[34]={name="opls_135",nameB="opls_135"} 55: type[35]={name="opls_140",nameB="opls_140"} 55: type[36]={name="opls_140",nameB="opls_140"} 55: type[37]={name="opls_140",nameB="opls_140"} 55: type[38]={name="opls_235",nameB="opls_235"} 55: type[39]={name="opls_236",nameB="opls_236"} 55: type[40]={name="opls_238",nameB="opls_238"} 55: type[41]={name="opls_241",nameB="opls_241"} 55: type[42]={name="opls_224B",nameB="opls_224B"} 55: type[43]={name="opls_140",nameB="opls_140"} 55: type[44]={name="opls_149",nameB="opls_149"} 55: type[45]={name="opls_140",nameB="opls_140"} 55: type[46]={name="opls_140",nameB="opls_140"} 55: type[47]={name="opls_145",nameB="opls_145"} 55: type[48]={name="opls_145",nameB="opls_145"} 55: type[49]={name="opls_146",nameB="opls_146"} 55: type[50]={name="opls_145",nameB="opls_145"} 55: type[51]={name="opls_146",nameB="opls_146"} 55: type[52]={name="opls_145",nameB="opls_145"} 55: type[53]={name="opls_146",nameB="opls_146"} 55: type[54]={name="opls_145",nameB="opls_145"} 55: type[55]={name="opls_146",nameB="opls_146"} 55: type[56]={name="opls_145",nameB="opls_145"} 55: type[57]={name="opls_146",nameB="opls_146"} 55: type[58]={name="opls_235",nameB="opls_235"} 55: type[59]={name="opls_236",nameB="opls_236"} 55: type[60]={name="opls_238",nameB="opls_238"} 55: type[61]={name="opls_241",nameB="opls_241"} 55: type[62]={name="opls_223B",nameB="opls_223B"} 55: type[63]={name="opls_140",nameB="opls_140"} 55: type[64]={name="opls_140",nameB="opls_140"} 55: type[65]={name="opls_235",nameB="opls_235"} 55: type[66]={name="opls_236",nameB="opls_236"} 55: type[67]={name="opls_238",nameB="opls_238"} 55: type[68]={name="opls_241",nameB="opls_241"} 55: type[69]={name="opls_224B",nameB="opls_224B"} 55: type[70]={name="opls_140",nameB="opls_140"} 55: type[71]={name="opls_136",nameB="opls_136"} 55: type[72]={name="opls_140",nameB="opls_140"} 55: type[73]={name="opls_140",nameB="opls_140"} 55: type[74]={name="opls_308",nameB="opls_308"} 55: type[75]={name="opls_140",nameB="opls_140"} 55: type[76]={name="opls_140",nameB="opls_140"} 55: type[77]={name="opls_307",nameB="opls_307"} 55: type[78]={name="opls_140",nameB="opls_140"} 55: type[79]={name="opls_140",nameB="opls_140"} 55: type[80]={name="opls_303",nameB="opls_303"} 55: type[81]={name="opls_304",nameB="opls_304"} 55: type[82]={name="opls_302",nameB="opls_302"} 55: type[83]={name="opls_300",nameB="opls_300"} 55: type[84]={name="opls_301",nameB="opls_301"} 55: type[85]={name="opls_301",nameB="opls_301"} 55: type[86]={name="opls_300",nameB="opls_300"} 55: type[87]={name="opls_301",nameB="opls_301"} 55: type[88]={name="opls_301",nameB="opls_301"} 55: type[89]={name="opls_235",nameB="opls_235"} 55: type[90]={name="opls_236",nameB="opls_236"} 55: type[91]={name="opls_238",nameB="opls_238"} 55: type[92]={name="opls_241",nameB="opls_241"} 55: type[93]={name="opls_224B",nameB="opls_224B"} 55: type[94]={name="opls_140",nameB="opls_140"} 55: type[95]={name="opls_206",nameB="opls_206"} 55: type[96]={name="opls_140",nameB="opls_140"} 55: type[97]={name="opls_140",nameB="opls_140"} 55: type[98]={name="opls_200",nameB="opls_200"} 55: type[99]={name="opls_204",nameB="opls_204"} 55: type[100]={name="opls_235",nameB="opls_235"} 55: type[101]={name="opls_236",nameB="opls_236"} 55: type[102]={name="opls_238",nameB="opls_238"} 55: type[103]={name="opls_241",nameB="opls_241"} 55: type[104]={name="opls_224B",nameB="opls_224B"} 55: type[105]={name="opls_140",nameB="opls_140"} 55: type[106]={name="opls_136",nameB="opls_136"} 55: type[107]={name="opls_140",nameB="opls_140"} 55: type[108]={name="opls_140",nameB="opls_140"} 55: type[109]={name="opls_274",nameB="opls_274"} 55: type[110]={name="opls_140",nameB="opls_140"} 55: type[111]={name="opls_140",nameB="opls_140"} 55: type[112]={name="opls_271",nameB="opls_271"} 55: type[113]={name="opls_272",nameB="opls_272"} 55: type[114]={name="opls_272",nameB="opls_272"} 55: type[115]={name="opls_235",nameB="opls_235"} 55: type[116]={name="opls_236",nameB="opls_236"} 55: type[117]={name="opls_238",nameB="opls_238"} 55: type[118]={name="opls_241",nameB="opls_241"} 55: type[119]={name="opls_224B",nameB="opls_224B"} 55: type[120]={name="opls_140",nameB="opls_140"} 55: type[121]={name="opls_136",nameB="opls_136"} 55: type[122]={name="opls_140",nameB="opls_140"} 55: type[123]={name="opls_140",nameB="opls_140"} 55: type[124]={name="opls_137",nameB="opls_137"} 55: type[125]={name="opls_140",nameB="opls_140"} 55: type[126]={name="opls_135",nameB="opls_135"} 55: type[127]={name="opls_140",nameB="opls_140"} 55: type[128]={name="opls_140",nameB="opls_140"} 55: type[129]={name="opls_140",nameB="opls_140"} 55: type[130]={name="opls_135",nameB="opls_135"} 55: type[131]={name="opls_140",nameB="opls_140"} 55: type[132]={name="opls_140",nameB="opls_140"} 55: type[133]={name="opls_140",nameB="opls_140"} 55: type[134]={name="opls_235",nameB="opls_235"} 55: type[135]={name="opls_236",nameB="opls_236"} 55: type[136]={name="opls_238",nameB="opls_238"} 55: type[137]={name="opls_241",nameB="opls_241"} 55: type[138]={name="opls_224B",nameB="opls_224B"} 55: type[139]={name="opls_140",nameB="opls_140"} 55: type[140]={name="opls_135",nameB="opls_135"} 55: type[141]={name="opls_140",nameB="opls_140"} 55: type[142]={name="opls_140",nameB="opls_140"} 55: type[143]={name="opls_140",nameB="opls_140"} 55: type[144]={name="opls_235",nameB="opls_235"} 55: type[145]={name="opls_236",nameB="opls_236"} 55: type[146]={name="opls_238",nameB="opls_238"} 55: type[147]={name="opls_241",nameB="opls_241"} 55: type[148]={name="opls_224B",nameB="opls_224B"} 55: type[149]={name="opls_140",nameB="opls_140"} 55: type[150]={name="opls_135",nameB="opls_135"} 55: type[151]={name="opls_140",nameB="opls_140"} 55: type[152]={name="opls_140",nameB="opls_140"} 55: type[153]={name="opls_140",nameB="opls_140"} 55: type[154]={name="opls_235",nameB="opls_235"} 55: type[155]={name="opls_236",nameB="opls_236"} 55: residue (10): 55: residue[0]={name="LYS", nr=1, ic=' '} 55: residue[1]={name="VAL", nr=2, ic=' '} 55: residue[2]={name="PHE", nr=3, ic=' '} 55: residue[3]={name="GLY", nr=4, ic=' '} 55: residue[4]={name="ARG", nr=5, ic=' '} 55: residue[5]={name="CYS", nr=6, ic=' '} 55: residue[6]={name="GLU", nr=7, ic=' '} 55: residue[7]={name="LEU", nr=8, ic=' '} 55: residue[8]={name="ALA", nr=9, ic=' '} 55: residue[9]={name="ALA", nr=10, ic=' '} 55: excls: 55: numLists=156 55: numElements=1828 55: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 55: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 55: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 55: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 55: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 55: 23, 24, 25, 26} 55: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 55: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 55: 14, 15, 22, 23, 24} 55: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 55: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 55: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 55: 16, 17, 18, 22} 55: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 55: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 55: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 55: 17, 18, 19, 20, 21} 55: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 55: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 55: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 55: 20, 21} 55: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 55: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 55: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 55: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 55: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 55: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 55: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 55: 26, 27, 28, 38} 55: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 55: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 55: 30, 34, 38, 39, 40} 55: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 55: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 55: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 55: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 55: 40} 55: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 55: 34, 35, 36, 37, 38, 39, 40} 55: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55: 36, 37, 38} 55: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55: 36, 37, 38} 55: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 55: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 55: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 55: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55: 36, 37, 38} 55: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 55: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 55: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 55: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 55: 40, 41, 42, 43, 44, 58} 55: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 55: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 55: 45, 46, 47, 58, 59, 60} 55: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 55: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 55: 48, 50, 58, 59, 60, 61, 62} 55: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 55: 60} 55: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55: 50, 51, 52, 54, 58, 59, 60} 55: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 55: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 55: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 55: 52, 53, 54, 55, 56, 58} 55: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55: 54, 56, 57} 55: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 55: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55: 55, 56, 57} 55: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 55: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 55: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 55: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 55: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 55: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 55: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 55: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 55: 60, 61, 62, 63, 64, 65} 55: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 55: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 55: 65, 66, 67} 55: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 55: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 55: 68, 69} 55: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 55: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 55: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 55: 70, 71, 89} 55: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 55: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 55: 72, 73, 74, 89, 90, 91} 55: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 55: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 55: 75, 76, 77, 89, 90, 91, 92, 93} 55: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 55: 91} 55: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 55: 77, 78, 79, 80, 89, 90, 91} 55: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 55: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 55: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 55: 79, 80, 81, 82, 89} 55: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 55: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 55: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 55: 81, 82, 83, 86} 55: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 55: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 55: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 55: 84, 85, 86, 87, 88} 55: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 55: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 55: 87, 88} 55: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 55: excls[84][num=6]={80, 82, 83, 84, 85, 86} 55: excls[85][num=6]={80, 82, 83, 84, 85, 86} 55: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 55: excls[87][num=6]={80, 82, 83, 86, 87, 88} 55: excls[88][num=6]={80, 82, 83, 86, 87, 88} 55: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 55: 91, 92, 93, 94, 95, 100} 55: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 55: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 55: 96, 97, 98, 100, 101, 102} 55: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 55: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 55: 99, 100, 101, 102, 103, 104} 55: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 55: 102} 55: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 55: 101, 102} 55: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 55: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 55: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 55: excls[99][num=6]={93, 95, 96, 97, 98, 99} 55: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 55: 102, 103, 104, 105, 106, 115} 55: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 55: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 55: 106, 107, 108, 109, 115, 116, 117} 55: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 55: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 55: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 55: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 55: 115, 116, 117} 55: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 55: 110, 111, 112, 113, 114, 115, 116, 117} 55: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 55: 112, 115} 55: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 55: 112, 115} 55: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 55: 112, 113, 114, 115} 55: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 55: 114} 55: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 55: 114} 55: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 55: 114} 55: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 55: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 55: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 55: 115, 116, 117, 118, 119, 120, 121, 134} 55: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 55: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 55: 120, 121, 122, 123, 124, 134, 135, 136} 55: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 55: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 55: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 55: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 55: 134, 135, 136} 55: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 55: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 55: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 55: 130, 134} 55: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 55: 130, 134} 55: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 55: 127, 128, 129, 130, 131, 132, 133, 134} 55: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 55: 129, 130, 131, 132, 133} 55: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 55: 129, 130, 131, 132, 133} 55: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 55: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 55: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 55: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 55: 129, 130, 131, 132, 133} 55: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 55: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 55: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 55: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 55: 134, 135, 136, 137, 138, 139, 140, 144} 55: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 55: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 55: 139, 140, 141, 142, 143, 144, 145, 146} 55: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 55: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 55: 142, 143, 144, 145, 146, 147, 148} 55: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 55: 144, 145, 146} 55: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 55: 144, 145, 146} 55: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 55: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 55: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 55: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 55: 144, 145, 146, 147, 148, 149, 150, 154} 55: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 55: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 55: 149, 150, 151, 152, 153, 154, 155} 55: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 55: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 55: 152, 153, 154, 155} 55: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 55: 154, 155} 55: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 55: 154, 155} 55: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 55: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 55: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 55: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 55: 154, 155} 55: excls[155][num=6]={146, 148, 149, 150, 154, 155} 55: Bond: 55: nr: 468 55: iatoms: 55: 0 type=100 (BONDS) 0 1 55: 1 type=100 (BONDS) 0 2 55: 2 type=100 (BONDS) 0 3 55: 3 type=101 (BONDS) 0 4 55: 4 type=102 (BONDS) 4 5 55: 5 type=103 (BONDS) 4 6 55: 6 type=104 (BONDS) 4 22 55: 7 type=102 (BONDS) 6 7 55: 8 type=102 (BONDS) 6 8 55: 9 type=103 (BONDS) 6 9 55: 10 type=102 (BONDS) 9 10 55: 11 type=102 (BONDS) 9 11 55: 12 type=103 (BONDS) 9 12 55: 13 type=102 (BONDS) 12 13 55: 14 type=102 (BONDS) 12 14 55: 15 type=103 (BONDS) 12 15 55: 16 type=102 (BONDS) 15 16 55: 17 type=102 (BONDS) 15 17 55: 18 type=101 (BONDS) 15 18 55: 19 type=100 (BONDS) 18 19 55: 20 type=100 (BONDS) 18 20 55: 21 type=100 (BONDS) 18 21 55: 22 type=105 (BONDS) 22 23 55: 23 type=106 (BONDS) 22 24 55: 24 type=100 (BONDS) 24 25 55: 25 type=107 (BONDS) 24 26 55: 26 type=102 (BONDS) 26 27 55: 27 type=103 (BONDS) 26 28 55: 28 type=104 (BONDS) 26 38 55: 29 type=102 (BONDS) 28 29 55: 30 type=103 (BONDS) 28 30 55: 31 type=103 (BONDS) 28 34 55: 32 type=102 (BONDS) 30 31 55: 33 type=102 (BONDS) 30 32 55: 34 type=102 (BONDS) 30 33 55: 35 type=102 (BONDS) 34 35 55: 36 type=102 (BONDS) 34 36 55: 37 type=102 (BONDS) 34 37 55: 38 type=105 (BONDS) 38 39 55: 39 type=106 (BONDS) 38 40 55: 40 type=100 (BONDS) 40 41 55: 41 type=107 (BONDS) 40 42 55: 42 type=102 (BONDS) 42 43 55: 43 type=103 (BONDS) 42 44 55: 44 type=104 (BONDS) 42 58 55: 45 type=102 (BONDS) 44 45 55: 46 type=102 (BONDS) 44 46 55: 47 type=108 (BONDS) 44 47 55: 48 type=109 (BONDS) 47 48 55: 49 type=109 (BONDS) 47 50 55: 50 type=110 (BONDS) 48 49 55: 51 type=109 (BONDS) 48 52 55: 52 type=110 (BONDS) 50 51 55: 53 type=109 (BONDS) 50 54 55: 54 type=110 (BONDS) 52 53 55: 55 type=109 (BONDS) 52 56 55: 56 type=110 (BONDS) 54 55 55: 57 type=109 (BONDS) 54 56 55: 58 type=110 (BONDS) 56 57 55: 59 type=105 (BONDS) 58 59 55: 60 type=106 (BONDS) 58 60 55: 61 type=100 (BONDS) 60 61 55: 62 type=107 (BONDS) 60 62 55: 63 type=102 (BONDS) 62 63 55: 64 type=102 (BONDS) 62 64 55: 65 type=104 (BONDS) 62 65 55: 66 type=105 (BONDS) 65 66 55: 67 type=106 (BONDS) 65 67 55: 68 type=100 (BONDS) 67 68 55: 69 type=107 (BONDS) 67 69 55: 70 type=102 (BONDS) 69 70 55: 71 type=103 (BONDS) 69 71 55: 72 type=104 (BONDS) 69 89 55: 73 type=102 (BONDS) 71 72 55: 74 type=102 (BONDS) 71 73 55: 75 type=103 (BONDS) 71 74 55: 76 type=102 (BONDS) 74 75 55: 77 type=102 (BONDS) 74 76 55: 78 type=103 (BONDS) 74 77 55: 79 type=102 (BONDS) 77 78 55: 80 type=102 (BONDS) 77 79 55: 81 type=111 (BONDS) 77 80 55: 82 type=100 (BONDS) 80 81 55: 83 type=112 (BONDS) 80 82 55: 84 type=112 (BONDS) 82 83 55: 85 type=112 (BONDS) 82 86 55: 86 type=100 (BONDS) 83 84 55: 87 type=100 (BONDS) 83 85 55: 88 type=100 (BONDS) 86 87 55: 89 type=100 (BONDS) 86 88 55: 90 type=105 (BONDS) 89 90 55: 91 type=106 (BONDS) 89 91 55: 92 type=100 (BONDS) 91 92 55: 93 type=107 (BONDS) 91 93 55: 94 type=102 (BONDS) 93 94 55: 95 type=103 (BONDS) 93 95 55: 96 type=104 (BONDS) 93 100 55: 97 type=102 (BONDS) 95 96 55: 98 type=102 (BONDS) 95 97 55: 99 type=113 (BONDS) 95 98 55: 100 type=114 (BONDS) 98 99 55: 101 type=105 (BONDS) 100 101 55: 102 type=106 (BONDS) 100 102 55: 103 type=100 (BONDS) 102 103 55: 104 type=107 (BONDS) 102 104 55: 105 type=102 (BONDS) 104 105 55: 106 type=103 (BONDS) 104 106 55: 107 type=104 (BONDS) 104 115 55: 108 type=102 (BONDS) 106 107 55: 109 type=102 (BONDS) 106 108 55: 110 type=103 (BONDS) 106 109 55: 111 type=102 (BONDS) 109 110 55: 112 type=102 (BONDS) 109 111 55: 113 type=104 (BONDS) 109 112 55: 114 type=115 (BONDS) 112 113 55: 115 type=115 (BONDS) 112 114 55: 116 type=105 (BONDS) 115 116 55: 117 type=106 (BONDS) 115 117 55: 118 type=100 (BONDS) 117 118 55: 119 type=107 (BONDS) 117 119 55: 120 type=102 (BONDS) 119 120 55: 121 type=103 (BONDS) 119 121 55: 122 type=104 (BONDS) 119 134 55: 123 type=102 (BONDS) 121 122 55: 124 type=102 (BONDS) 121 123 55: 125 type=103 (BONDS) 121 124 55: 126 type=102 (BONDS) 124 125 55: 127 type=103 (BONDS) 124 126 55: 128 type=103 (BONDS) 124 130 55: 129 type=102 (BONDS) 126 127 55: 130 type=102 (BONDS) 126 128 55: 131 type=102 (BONDS) 126 129 55: 132 type=102 (BONDS) 130 131 55: 133 type=102 (BONDS) 130 132 55: 134 type=102 (BONDS) 130 133 55: 135 type=105 (BONDS) 134 135 55: 136 type=106 (BONDS) 134 136 55: 137 type=100 (BONDS) 136 137 55: 138 type=107 (BONDS) 136 138 55: 139 type=102 (BONDS) 138 139 55: 140 type=103 (BONDS) 138 140 55: 141 type=104 (BONDS) 138 144 55: 142 type=102 (BONDS) 140 141 55: 143 type=102 (BONDS) 140 142 55: 144 type=102 (BONDS) 140 143 55: 145 type=105 (BONDS) 144 145 55: 146 type=106 (BONDS) 144 146 55: 147 type=100 (BONDS) 146 147 55: 148 type=107 (BONDS) 146 148 55: 149 type=102 (BONDS) 148 149 55: 150 type=103 (BONDS) 148 150 55: 151 type=104 (BONDS) 148 154 55: 152 type=102 (BONDS) 150 151 55: 153 type=102 (BONDS) 150 152 55: 154 type=102 (BONDS) 150 153 55: 155 type=105 (BONDS) 154 155 55: G96Bond: 55: nr: 0 55: Morse: 55: nr: 0 55: Cubic Bonds: 55: nr: 0 55: Connect Bonds: 55: nr: 0 55: Harmonic Pot.: 55: nr: 0 55: FENE Bonds: 55: nr: 0 55: Tab. Bonds: 55: nr: 0 55: Tab. Bonds NC: 55: nr: 0 55: Restraint Pot.: 55: nr: 0 55: Angle: 55: nr: 1124 55: iatoms: 55: 0 type=116 (ANGLES) 1 0 2 55: 1 type=116 (ANGLES) 1 0 3 55: 2 type=116 (ANGLES) 1 0 4 55: 3 type=116 (ANGLES) 2 0 3 55: 4 type=116 (ANGLES) 2 0 4 55: 5 type=116 (ANGLES) 3 0 4 55: 6 type=116 (ANGLES) 0 4 5 55: 7 type=117 (ANGLES) 0 4 6 55: 8 type=117 (ANGLES) 0 4 22 55: 9 type=118 (ANGLES) 5 4 6 55: 10 type=116 (ANGLES) 5 4 22 55: 11 type=119 (ANGLES) 6 4 22 55: 12 type=118 (ANGLES) 4 6 7 55: 13 type=118 (ANGLES) 4 6 8 55: 14 type=120 (ANGLES) 4 6 9 55: 15 type=121 (ANGLES) 7 6 8 55: 16 type=118 (ANGLES) 7 6 9 55: 17 type=118 (ANGLES) 8 6 9 55: 18 type=118 (ANGLES) 6 9 10 55: 19 type=118 (ANGLES) 6 9 11 55: 20 type=120 (ANGLES) 6 9 12 55: 21 type=121 (ANGLES) 10 9 11 55: 22 type=118 (ANGLES) 10 9 12 55: 23 type=118 (ANGLES) 11 9 12 55: 24 type=118 (ANGLES) 9 12 13 55: 25 type=118 (ANGLES) 9 12 14 55: 26 type=120 (ANGLES) 9 12 15 55: 27 type=121 (ANGLES) 13 12 14 55: 28 type=118 (ANGLES) 13 12 15 55: 29 type=118 (ANGLES) 14 12 15 55: 30 type=118 (ANGLES) 12 15 16 55: 31 type=118 (ANGLES) 12 15 17 55: 32 type=117 (ANGLES) 12 15 18 55: 33 type=121 (ANGLES) 16 15 17 55: 34 type=116 (ANGLES) 16 15 18 55: 35 type=116 (ANGLES) 17 15 18 55: 36 type=116 (ANGLES) 15 18 19 55: 37 type=116 (ANGLES) 15 18 20 55: 38 type=116 (ANGLES) 15 18 21 55: 39 type=116 (ANGLES) 19 18 20 55: 40 type=116 (ANGLES) 19 18 21 55: 41 type=116 (ANGLES) 20 18 21 55: 42 type=122 (ANGLES) 4 22 23 55: 43 type=123 (ANGLES) 4 22 24 55: 44 type=124 (ANGLES) 23 22 24 55: 45 type=125 (ANGLES) 22 24 25 55: 46 type=126 (ANGLES) 22 24 26 55: 47 type=127 (ANGLES) 25 24 26 55: 48 type=116 (ANGLES) 24 26 27 55: 49 type=128 (ANGLES) 24 26 28 55: 50 type=129 (ANGLES) 24 26 38 55: 51 type=118 (ANGLES) 27 26 28 55: 52 type=116 (ANGLES) 27 26 38 55: 53 type=119 (ANGLES) 28 26 38 55: 54 type=118 (ANGLES) 26 28 29 55: 55 type=120 (ANGLES) 26 28 30 55: 56 type=120 (ANGLES) 26 28 34 55: 57 type=118 (ANGLES) 29 28 30 55: 58 type=118 (ANGLES) 29 28 34 55: 59 type=120 (ANGLES) 30 28 34 55: 60 type=118 (ANGLES) 28 30 31 55: 61 type=118 (ANGLES) 28 30 32 55: 62 type=118 (ANGLES) 28 30 33 55: 63 type=121 (ANGLES) 31 30 32 55: 64 type=121 (ANGLES) 31 30 33 55: 65 type=121 (ANGLES) 32 30 33 55: 66 type=118 (ANGLES) 28 34 35 55: 67 type=118 (ANGLES) 28 34 36 55: 68 type=118 (ANGLES) 28 34 37 55: 69 type=121 (ANGLES) 35 34 36 55: 70 type=121 (ANGLES) 35 34 37 55: 71 type=121 (ANGLES) 36 34 37 55: 72 type=122 (ANGLES) 26 38 39 55: 73 type=123 (ANGLES) 26 38 40 55: 74 type=124 (ANGLES) 39 38 40 55: 75 type=125 (ANGLES) 38 40 41 55: 76 type=126 (ANGLES) 38 40 42 55: 77 type=127 (ANGLES) 41 40 42 55: 78 type=116 (ANGLES) 40 42 43 55: 79 type=128 (ANGLES) 40 42 44 55: 80 type=129 (ANGLES) 40 42 58 55: 81 type=118 (ANGLES) 43 42 44 55: 82 type=116 (ANGLES) 43 42 58 55: 83 type=119 (ANGLES) 44 42 58 55: 84 type=118 (ANGLES) 42 44 45 55: 85 type=118 (ANGLES) 42 44 46 55: 86 type=130 (ANGLES) 42 44 47 55: 87 type=121 (ANGLES) 45 44 46 55: 88 type=116 (ANGLES) 45 44 47 55: 89 type=116 (ANGLES) 46 44 47 55: 90 type=131 (ANGLES) 44 47 48 55: 91 type=131 (ANGLES) 44 47 50 55: 92 type=132 (ANGLES) 48 47 50 55: 93 type=133 (ANGLES) 47 48 49 55: 94 type=132 (ANGLES) 47 48 52 55: 95 type=133 (ANGLES) 49 48 52 55: 96 type=133 (ANGLES) 47 50 51 55: 97 type=132 (ANGLES) 47 50 54 55: 98 type=133 (ANGLES) 51 50 54 55: 99 type=133 (ANGLES) 48 52 53 55: 100 type=132 (ANGLES) 48 52 56 55: 101 type=133 (ANGLES) 53 52 56 55: 102 type=133 (ANGLES) 50 54 55 55: 103 type=132 (ANGLES) 50 54 56 55: 104 type=133 (ANGLES) 55 54 56 55: 105 type=132 (ANGLES) 52 56 54 55: 106 type=133 (ANGLES) 52 56 57 55: 107 type=133 (ANGLES) 54 56 57 55: 108 type=122 (ANGLES) 42 58 59 55: 109 type=123 (ANGLES) 42 58 60 55: 110 type=124 (ANGLES) 59 58 60 55: 111 type=125 (ANGLES) 58 60 61 55: 112 type=126 (ANGLES) 58 60 62 55: 113 type=127 (ANGLES) 61 60 62 55: 114 type=116 (ANGLES) 60 62 63 55: 115 type=116 (ANGLES) 60 62 64 55: 116 type=129 (ANGLES) 60 62 65 55: 117 type=121 (ANGLES) 63 62 64 55: 118 type=116 (ANGLES) 63 62 65 55: 119 type=116 (ANGLES) 64 62 65 55: 120 type=122 (ANGLES) 62 65 66 55: 121 type=123 (ANGLES) 62 65 67 55: 122 type=124 (ANGLES) 66 65 67 55: 123 type=125 (ANGLES) 65 67 68 55: 124 type=126 (ANGLES) 65 67 69 55: 125 type=127 (ANGLES) 68 67 69 55: 126 type=116 (ANGLES) 67 69 70 55: 127 type=128 (ANGLES) 67 69 71 55: 128 type=129 (ANGLES) 67 69 89 55: 129 type=118 (ANGLES) 70 69 71 55: 130 type=116 (ANGLES) 70 69 89 55: 131 type=119 (ANGLES) 71 69 89 55: 132 type=118 (ANGLES) 69 71 72 55: 133 type=118 (ANGLES) 69 71 73 55: 134 type=120 (ANGLES) 69 71 74 55: 135 type=121 (ANGLES) 72 71 73 55: 136 type=118 (ANGLES) 72 71 74 55: 137 type=118 (ANGLES) 73 71 74 55: 138 type=118 (ANGLES) 71 74 75 55: 139 type=118 (ANGLES) 71 74 76 55: 140 type=120 (ANGLES) 71 74 77 55: 141 type=121 (ANGLES) 75 74 76 55: 142 type=118 (ANGLES) 75 74 77 55: 143 type=118 (ANGLES) 76 74 77 55: 144 type=118 (ANGLES) 74 77 78 55: 145 type=118 (ANGLES) 74 77 79 55: 146 type=117 (ANGLES) 74 77 80 55: 147 type=121 (ANGLES) 78 77 79 55: 148 type=116 (ANGLES) 78 77 80 55: 149 type=116 (ANGLES) 79 77 80 55: 150 type=134 (ANGLES) 77 80 81 55: 151 type=135 (ANGLES) 77 80 82 55: 152 type=133 (ANGLES) 81 80 82 55: 153 type=131 (ANGLES) 80 82 83 55: 154 type=131 (ANGLES) 80 82 86 55: 155 type=131 (ANGLES) 83 82 86 55: 156 type=133 (ANGLES) 82 83 84 55: 157 type=133 (ANGLES) 82 83 85 55: 158 type=133 (ANGLES) 84 83 85 55: 159 type=133 (ANGLES) 82 86 87 55: 160 type=133 (ANGLES) 82 86 88 55: 161 type=133 (ANGLES) 87 86 88 55: 162 type=122 (ANGLES) 69 89 90 55: 163 type=123 (ANGLES) 69 89 91 55: 164 type=124 (ANGLES) 90 89 91 55: 165 type=125 (ANGLES) 89 91 92 55: 166 type=126 (ANGLES) 89 91 93 55: 167 type=127 (ANGLES) 92 91 93 55: 168 type=116 (ANGLES) 91 93 94 55: 169 type=128 (ANGLES) 91 93 95 55: 170 type=129 (ANGLES) 91 93 100 55: 171 type=118 (ANGLES) 94 93 95 55: 172 type=116 (ANGLES) 94 93 100 55: 173 type=119 (ANGLES) 95 93 100 55: 174 type=118 (ANGLES) 93 95 96 55: 175 type=118 (ANGLES) 93 95 97 55: 176 type=136 (ANGLES) 93 95 98 55: 177 type=121 (ANGLES) 96 95 97 55: 178 type=116 (ANGLES) 96 95 98 55: 179 type=116 (ANGLES) 97 95 98 55: 180 type=137 (ANGLES) 95 98 99 55: 181 type=122 (ANGLES) 93 100 101 55: 182 type=123 (ANGLES) 93 100 102 55: 183 type=124 (ANGLES) 101 100 102 55: 184 type=125 (ANGLES) 100 102 103 55: 185 type=126 (ANGLES) 100 102 104 55: 186 type=127 (ANGLES) 103 102 104 55: 187 type=116 (ANGLES) 102 104 105 55: 188 type=128 (ANGLES) 102 104 106 55: 189 type=129 (ANGLES) 102 104 115 55: 190 type=118 (ANGLES) 105 104 106 55: 191 type=116 (ANGLES) 105 104 115 55: 192 type=119 (ANGLES) 106 104 115 55: 193 type=118 (ANGLES) 104 106 107 55: 194 type=118 (ANGLES) 104 106 108 55: 195 type=120 (ANGLES) 104 106 109 55: 196 type=121 (ANGLES) 107 106 108 55: 197 type=118 (ANGLES) 107 106 109 55: 198 type=118 (ANGLES) 108 106 109 55: 199 type=118 (ANGLES) 106 109 110 55: 200 type=118 (ANGLES) 106 109 111 55: 201 type=119 (ANGLES) 106 109 112 55: 202 type=121 (ANGLES) 110 109 111 55: 203 type=116 (ANGLES) 110 109 112 55: 204 type=116 (ANGLES) 111 109 112 55: 205 type=138 (ANGLES) 109 112 113 55: 206 type=138 (ANGLES) 109 112 114 55: 207 type=139 (ANGLES) 113 112 114 55: 208 type=122 (ANGLES) 104 115 116 55: 209 type=123 (ANGLES) 104 115 117 55: 210 type=124 (ANGLES) 116 115 117 55: 211 type=125 (ANGLES) 115 117 118 55: 212 type=126 (ANGLES) 115 117 119 55: 213 type=127 (ANGLES) 118 117 119 55: 214 type=116 (ANGLES) 117 119 120 55: 215 type=128 (ANGLES) 117 119 121 55: 216 type=129 (ANGLES) 117 119 134 55: 217 type=118 (ANGLES) 120 119 121 55: 218 type=116 (ANGLES) 120 119 134 55: 219 type=119 (ANGLES) 121 119 134 55: 220 type=118 (ANGLES) 119 121 122 55: 221 type=118 (ANGLES) 119 121 123 55: 222 type=120 (ANGLES) 119 121 124 55: 223 type=121 (ANGLES) 122 121 123 55: 224 type=118 (ANGLES) 122 121 124 55: 225 type=118 (ANGLES) 123 121 124 55: 226 type=118 (ANGLES) 121 124 125 55: 227 type=120 (ANGLES) 121 124 126 55: 228 type=120 (ANGLES) 121 124 130 55: 229 type=118 (ANGLES) 125 124 126 55: 230 type=118 (ANGLES) 125 124 130 55: 231 type=120 (ANGLES) 126 124 130 55: 232 type=118 (ANGLES) 124 126 127 55: 233 type=118 (ANGLES) 124 126 128 55: 234 type=118 (ANGLES) 124 126 129 55: 235 type=121 (ANGLES) 127 126 128 55: 236 type=121 (ANGLES) 127 126 129 55: 237 type=121 (ANGLES) 128 126 129 55: 238 type=118 (ANGLES) 124 130 131 55: 239 type=118 (ANGLES) 124 130 132 55: 240 type=118 (ANGLES) 124 130 133 55: 241 type=121 (ANGLES) 131 130 132 55: 242 type=121 (ANGLES) 131 130 133 55: 243 type=121 (ANGLES) 132 130 133 55: 244 type=122 (ANGLES) 119 134 135 55: 245 type=123 (ANGLES) 119 134 136 55: 246 type=124 (ANGLES) 135 134 136 55: 247 type=125 (ANGLES) 134 136 137 55: 248 type=126 (ANGLES) 134 136 138 55: 249 type=127 (ANGLES) 137 136 138 55: 250 type=116 (ANGLES) 136 138 139 55: 251 type=128 (ANGLES) 136 138 140 55: 252 type=129 (ANGLES) 136 138 144 55: 253 type=118 (ANGLES) 139 138 140 55: 254 type=116 (ANGLES) 139 138 144 55: 255 type=119 (ANGLES) 140 138 144 55: 256 type=118 (ANGLES) 138 140 141 55: 257 type=118 (ANGLES) 138 140 142 55: 258 type=118 (ANGLES) 138 140 143 55: 259 type=121 (ANGLES) 141 140 142 55: 260 type=121 (ANGLES) 141 140 143 55: 261 type=121 (ANGLES) 142 140 143 55: 262 type=122 (ANGLES) 138 144 145 55: 263 type=123 (ANGLES) 138 144 146 55: 264 type=124 (ANGLES) 145 144 146 55: 265 type=125 (ANGLES) 144 146 147 55: 266 type=126 (ANGLES) 144 146 148 55: 267 type=127 (ANGLES) 147 146 148 55: 268 type=116 (ANGLES) 146 148 149 55: 269 type=128 (ANGLES) 146 148 150 55: 270 type=129 (ANGLES) 146 148 154 55: 271 type=118 (ANGLES) 149 148 150 55: 272 type=116 (ANGLES) 149 148 154 55: 273 type=119 (ANGLES) 150 148 154 55: 274 type=118 (ANGLES) 148 150 151 55: 275 type=118 (ANGLES) 148 150 152 55: 276 type=118 (ANGLES) 148 150 153 55: 277 type=121 (ANGLES) 151 150 152 55: 278 type=121 (ANGLES) 151 150 153 55: 279 type=121 (ANGLES) 152 150 153 55: 280 type=122 (ANGLES) 148 154 155 55: G96Angle: 55: nr: 0 55: Restr. Angles: 55: nr: 0 55: Lin. Angle: 55: nr: 0 55: Bond-Cross: 55: nr: 0 55: BA-Cross: 55: nr: 0 55: U-B: 55: nr: 0 55: Quartic Angles: 55: nr: 0 55: Tab. Angles: 55: nr: 0 55: Proper Dih.: 55: nr: 145 55: iatoms: 55: 0 type=140 (PDIHS) 4 24 22 23 55: 1 type=141 (PDIHS) 22 26 24 25 55: 2 type=140 (PDIHS) 26 40 38 39 55: 3 type=141 (PDIHS) 38 42 40 41 55: 4 type=140 (PDIHS) 42 60 58 59 55: 5 type=142 (PDIHS) 44 47 50 48 55: 6 type=142 (PDIHS) 47 52 48 49 55: 7 type=142 (PDIHS) 47 54 50 51 55: 8 type=142 (PDIHS) 48 56 52 53 55: 9 type=142 (PDIHS) 50 56 54 55 55: 10 type=142 (PDIHS) 52 54 56 57 55: 11 type=141 (PDIHS) 58 62 60 61 55: 12 type=140 (PDIHS) 62 67 65 66 55: 13 type=141 (PDIHS) 65 69 67 68 55: 14 type=140 (PDIHS) 69 91 89 90 55: 15 type=141 (PDIHS) 77 82 80 81 55: 16 type=140 (PDIHS) 80 83 82 86 55: 17 type=141 (PDIHS) 82 84 83 85 55: 18 type=141 (PDIHS) 82 87 86 88 55: 19 type=141 (PDIHS) 89 93 91 92 55: 20 type=140 (PDIHS) 93 102 100 101 55: 21 type=141 (PDIHS) 100 104 102 103 55: 22 type=140 (PDIHS) 104 117 115 116 55: 23 type=140 (PDIHS) 109 113 112 114 55: 24 type=141 (PDIHS) 115 119 117 118 55: 25 type=140 (PDIHS) 119 136 134 135 55: 26 type=141 (PDIHS) 134 138 136 137 55: 27 type=140 (PDIHS) 138 146 144 145 55: 28 type=141 (PDIHS) 144 148 146 147 55: Ryckaert-Bell.: 55: nr: 1565 55: iatoms: 55: 0 type=143 (RBDIHS) 1 0 4 5 55: 1 type=144 (RBDIHS) 1 0 4 6 55: 2 type=144 (RBDIHS) 1 0 4 22 55: 3 type=143 (RBDIHS) 2 0 4 5 55: 4 type=144 (RBDIHS) 2 0 4 6 55: 5 type=144 (RBDIHS) 2 0 4 22 55: 6 type=143 (RBDIHS) 3 0 4 5 55: 7 type=144 (RBDIHS) 3 0 4 6 55: 8 type=144 (RBDIHS) 3 0 4 22 55: 9 type=145 (RBDIHS) 0 4 6 9 55: 10 type=146 (RBDIHS) 22 4 6 9 55: 11 type=147 (RBDIHS) 0 4 6 7 55: 12 type=147 (RBDIHS) 0 4 6 8 55: 13 type=148 (RBDIHS) 5 4 6 7 55: 14 type=148 (RBDIHS) 5 4 6 8 55: 15 type=148 (RBDIHS) 5 4 6 9 55: 16 type=149 (RBDIHS) 22 4 6 7 55: 17 type=149 (RBDIHS) 22 4 6 8 55: 18 type=150 (RBDIHS) 0 4 22 24 55: 19 type=151 (RBDIHS) 6 4 22 24 55: 20 type=148 (RBDIHS) 4 6 9 10 55: 21 type=148 (RBDIHS) 4 6 9 11 55: 22 type=152 (RBDIHS) 4 6 9 12 55: 23 type=148 (RBDIHS) 7 6 9 10 55: 24 type=148 (RBDIHS) 7 6 9 11 55: 25 type=148 (RBDIHS) 7 6 9 12 55: 26 type=148 (RBDIHS) 8 6 9 10 55: 27 type=148 (RBDIHS) 8 6 9 11 55: 28 type=148 (RBDIHS) 8 6 9 12 55: 29 type=148 (RBDIHS) 6 9 12 13 55: 30 type=148 (RBDIHS) 6 9 12 14 55: 31 type=152 (RBDIHS) 6 9 12 15 55: 32 type=148 (RBDIHS) 10 9 12 13 55: 33 type=148 (RBDIHS) 10 9 12 14 55: 34 type=148 (RBDIHS) 10 9 12 15 55: 35 type=148 (RBDIHS) 11 9 12 13 55: 36 type=148 (RBDIHS) 11 9 12 14 55: 37 type=148 (RBDIHS) 11 9 12 15 55: 38 type=148 (RBDIHS) 9 12 15 16 55: 39 type=148 (RBDIHS) 9 12 15 17 55: 40 type=153 (RBDIHS) 9 12 15 18 55: 41 type=148 (RBDIHS) 13 12 15 16 55: 42 type=148 (RBDIHS) 13 12 15 17 55: 43 type=154 (RBDIHS) 13 12 15 18 55: 44 type=148 (RBDIHS) 14 12 15 16 55: 45 type=148 (RBDIHS) 14 12 15 17 55: 46 type=154 (RBDIHS) 14 12 15 18 55: 47 type=144 (RBDIHS) 12 15 18 19 55: 48 type=144 (RBDIHS) 12 15 18 20 55: 49 type=144 (RBDIHS) 12 15 18 21 55: 50 type=143 (RBDIHS) 16 15 18 19 55: 51 type=143 (RBDIHS) 16 15 18 20 55: 52 type=143 (RBDIHS) 16 15 18 21 55: 53 type=143 (RBDIHS) 17 15 18 19 55: 54 type=143 (RBDIHS) 17 15 18 20 55: 55 type=143 (RBDIHS) 17 15 18 21 55: 56 type=155 (RBDIHS) 4 22 24 25 55: 57 type=156 (RBDIHS) 4 22 24 26 55: 58 type=155 (RBDIHS) 23 22 24 25 55: 59 type=157 (RBDIHS) 23 22 24 26 55: 60 type=158 (RBDIHS) 22 24 26 28 55: 61 type=159 (RBDIHS) 22 24 26 38 55: 62 type=160 (RBDIHS) 24 26 28 30 55: 63 type=160 (RBDIHS) 24 26 28 34 55: 64 type=161 (RBDIHS) 38 26 28 30 55: 65 type=161 (RBDIHS) 38 26 28 34 55: 66 type=147 (RBDIHS) 24 26 28 29 55: 67 type=148 (RBDIHS) 27 26 28 29 55: 68 type=148 (RBDIHS) 27 26 28 30 55: 69 type=148 (RBDIHS) 27 26 28 34 55: 70 type=149 (RBDIHS) 38 26 28 29 55: 71 type=150 (RBDIHS) 24 26 38 40 55: 72 type=151 (RBDIHS) 28 26 38 40 55: 73 type=148 (RBDIHS) 26 28 30 31 55: 74 type=148 (RBDIHS) 26 28 30 32 55: 75 type=148 (RBDIHS) 26 28 30 33 55: 76 type=148 (RBDIHS) 29 28 30 31 55: 77 type=148 (RBDIHS) 29 28 30 32 55: 78 type=148 (RBDIHS) 29 28 30 33 55: 79 type=148 (RBDIHS) 34 28 30 31 55: 80 type=148 (RBDIHS) 34 28 30 32 55: 81 type=148 (RBDIHS) 34 28 30 33 55: 82 type=148 (RBDIHS) 26 28 34 35 55: 83 type=148 (RBDIHS) 26 28 34 36 55: 84 type=148 (RBDIHS) 26 28 34 37 55: 85 type=148 (RBDIHS) 29 28 34 35 55: 86 type=148 (RBDIHS) 29 28 34 36 55: 87 type=148 (RBDIHS) 29 28 34 37 55: 88 type=148 (RBDIHS) 30 28 34 35 55: 89 type=148 (RBDIHS) 30 28 34 36 55: 90 type=148 (RBDIHS) 30 28 34 37 55: 91 type=155 (RBDIHS) 26 38 40 41 55: 92 type=156 (RBDIHS) 26 38 40 42 55: 93 type=155 (RBDIHS) 39 38 40 41 55: 94 type=157 (RBDIHS) 39 38 40 42 55: 95 type=158 (RBDIHS) 38 40 42 44 55: 96 type=159 (RBDIHS) 38 40 42 58 55: 97 type=147 (RBDIHS) 40 42 44 45 55: 98 type=147 (RBDIHS) 40 42 44 46 55: 99 type=162 (RBDIHS) 40 42 44 47 55: 100 type=148 (RBDIHS) 43 42 44 45 55: 101 type=148 (RBDIHS) 43 42 44 46 55: 102 type=163 (RBDIHS) 43 42 44 47 55: 103 type=149 (RBDIHS) 58 42 44 45 55: 104 type=149 (RBDIHS) 58 42 44 46 55: 105 type=164 (RBDIHS) 58 42 44 47 55: 106 type=150 (RBDIHS) 40 42 58 60 55: 107 type=151 (RBDIHS) 44 42 58 60 55: 108 type=165 (RBDIHS) 44 47 48 49 55: 109 type=165 (RBDIHS) 44 47 48 52 55: 110 type=165 (RBDIHS) 50 47 48 49 55: 111 type=165 (RBDIHS) 50 47 48 52 55: 112 type=165 (RBDIHS) 44 47 50 51 55: 113 type=165 (RBDIHS) 44 47 50 54 55: 114 type=165 (RBDIHS) 48 47 50 51 55: 115 type=165 (RBDIHS) 48 47 50 54 55: 116 type=165 (RBDIHS) 47 48 52 53 55: 117 type=165 (RBDIHS) 47 48 52 56 55: 118 type=165 (RBDIHS) 49 48 52 53 55: 119 type=165 (RBDIHS) 49 48 52 56 55: 120 type=165 (RBDIHS) 47 50 54 55 55: 121 type=165 (RBDIHS) 47 50 54 56 55: 122 type=165 (RBDIHS) 51 50 54 55 55: 123 type=165 (RBDIHS) 51 50 54 56 55: 124 type=165 (RBDIHS) 48 52 56 54 55: 125 type=165 (RBDIHS) 48 52 56 57 55: 126 type=165 (RBDIHS) 53 52 56 54 55: 127 type=165 (RBDIHS) 53 52 56 57 55: 128 type=165 (RBDIHS) 50 54 56 52 55: 129 type=165 (RBDIHS) 50 54 56 57 55: 130 type=165 (RBDIHS) 55 54 56 52 55: 131 type=165 (RBDIHS) 55 54 56 57 55: 132 type=155 (RBDIHS) 42 58 60 61 55: 133 type=156 (RBDIHS) 42 58 60 62 55: 134 type=155 (RBDIHS) 59 58 60 61 55: 135 type=157 (RBDIHS) 59 58 60 62 55: 136 type=159 (RBDIHS) 58 60 62 65 55: 137 type=150 (RBDIHS) 60 62 65 67 55: 138 type=155 (RBDIHS) 62 65 67 68 55: 139 type=156 (RBDIHS) 62 65 67 69 55: 140 type=155 (RBDIHS) 66 65 67 68 55: 141 type=157 (RBDIHS) 66 65 67 69 55: 142 type=158 (RBDIHS) 65 67 69 71 55: 143 type=159 (RBDIHS) 65 67 69 89 55: 144 type=166 (RBDIHS) 67 69 71 74 55: 145 type=167 (RBDIHS) 89 69 71 74 55: 146 type=147 (RBDIHS) 67 69 71 72 55: 147 type=147 (RBDIHS) 67 69 71 73 55: 148 type=148 (RBDIHS) 70 69 71 72 55: 149 type=148 (RBDIHS) 70 69 71 73 55: 150 type=148 (RBDIHS) 70 69 71 74 55: 151 type=149 (RBDIHS) 89 69 71 72 55: 152 type=149 (RBDIHS) 89 69 71 73 55: 153 type=150 (RBDIHS) 67 69 89 91 55: 154 type=151 (RBDIHS) 71 69 89 91 55: 155 type=148 (RBDIHS) 69 71 74 75 55: 156 type=148 (RBDIHS) 69 71 74 76 55: 157 type=152 (RBDIHS) 69 71 74 77 55: 158 type=148 (RBDIHS) 72 71 74 75 55: 159 type=148 (RBDIHS) 72 71 74 76 55: 160 type=148 (RBDIHS) 72 71 74 77 55: 161 type=148 (RBDIHS) 73 71 74 75 55: 162 type=148 (RBDIHS) 73 71 74 76 55: 163 type=148 (RBDIHS) 73 71 74 77 55: 164 type=148 (RBDIHS) 71 74 77 78 55: 165 type=148 (RBDIHS) 71 74 77 79 55: 166 type=153 (RBDIHS) 71 74 77 80 55: 167 type=148 (RBDIHS) 75 74 77 78 55: 168 type=148 (RBDIHS) 75 74 77 79 55: 169 type=168 (RBDIHS) 75 74 77 80 55: 170 type=148 (RBDIHS) 76 74 77 78 55: 171 type=148 (RBDIHS) 76 74 77 79 55: 172 type=168 (RBDIHS) 76 74 77 80 55: 173 type=169 (RBDIHS) 74 77 80 81 55: 174 type=170 (RBDIHS) 74 77 80 82 55: 175 type=171 (RBDIHS) 78 77 80 82 55: 176 type=171 (RBDIHS) 79 77 80 82 55: 177 type=172 (RBDIHS) 77 80 82 83 55: 178 type=172 (RBDIHS) 77 80 82 86 55: 179 type=173 (RBDIHS) 81 80 82 83 55: 180 type=173 (RBDIHS) 81 80 82 86 55: 181 type=173 (RBDIHS) 80 82 83 84 55: 182 type=173 (RBDIHS) 80 82 83 85 55: 183 type=173 (RBDIHS) 86 82 83 84 55: 184 type=173 (RBDIHS) 86 82 83 85 55: 185 type=173 (RBDIHS) 80 82 86 87 55: 186 type=173 (RBDIHS) 80 82 86 88 55: 187 type=173 (RBDIHS) 83 82 86 87 55: 188 type=173 (RBDIHS) 83 82 86 88 55: 189 type=155 (RBDIHS) 69 89 91 92 55: 190 type=156 (RBDIHS) 69 89 91 93 55: 191 type=155 (RBDIHS) 90 89 91 92 55: 192 type=157 (RBDIHS) 90 89 91 93 55: 193 type=158 (RBDIHS) 89 91 93 95 55: 194 type=159 (RBDIHS) 89 91 93 100 55: 195 type=174 (RBDIHS) 91 93 95 98 55: 196 type=175 (RBDIHS) 100 93 95 98 55: 197 type=147 (RBDIHS) 91 93 95 96 55: 198 type=147 (RBDIHS) 91 93 95 97 55: 199 type=148 (RBDIHS) 94 93 95 96 55: 200 type=148 (RBDIHS) 94 93 95 97 55: 201 type=176 (RBDIHS) 94 93 95 98 55: 202 type=149 (RBDIHS) 100 93 95 96 55: 203 type=149 (RBDIHS) 100 93 95 97 55: 204 type=150 (RBDIHS) 91 93 100 102 55: 205 type=151 (RBDIHS) 95 93 100 102 55: 206 type=177 (RBDIHS) 93 95 98 99 55: 207 type=178 (RBDIHS) 96 95 98 99 55: 208 type=178 (RBDIHS) 97 95 98 99 55: 209 type=155 (RBDIHS) 93 100 102 103 55: 210 type=156 (RBDIHS) 93 100 102 104 55: 211 type=155 (RBDIHS) 101 100 102 103 55: 212 type=157 (RBDIHS) 101 100 102 104 55: 213 type=158 (RBDIHS) 100 102 104 106 55: 214 type=159 (RBDIHS) 100 102 104 115 55: 215 type=179 (RBDIHS) 102 104 106 109 55: 216 type=180 (RBDIHS) 115 104 106 109 55: 217 type=147 (RBDIHS) 102 104 106 107 55: 218 type=147 (RBDIHS) 102 104 106 108 55: 219 type=148 (RBDIHS) 105 104 106 107 55: 220 type=148 (RBDIHS) 105 104 106 108 55: 221 type=148 (RBDIHS) 105 104 106 109 55: 222 type=149 (RBDIHS) 115 104 106 107 55: 223 type=149 (RBDIHS) 115 104 106 108 55: 224 type=150 (RBDIHS) 102 104 115 117 55: 225 type=151 (RBDIHS) 106 104 115 117 55: 226 type=148 (RBDIHS) 104 106 109 110 55: 227 type=148 (RBDIHS) 104 106 109 111 55: 228 type=181 (RBDIHS) 104 106 109 112 55: 229 type=148 (RBDIHS) 107 106 109 110 55: 230 type=148 (RBDIHS) 107 106 109 111 55: 231 type=182 (RBDIHS) 107 106 109 112 55: 232 type=148 (RBDIHS) 108 106 109 110 55: 233 type=148 (RBDIHS) 108 106 109 111 55: 234 type=182 (RBDIHS) 108 106 109 112 55: 235 type=183 (RBDIHS) 106 109 112 113 55: 236 type=183 (RBDIHS) 106 109 112 114 55: 237 type=155 (RBDIHS) 104 115 117 118 55: 238 type=156 (RBDIHS) 104 115 117 119 55: 239 type=155 (RBDIHS) 116 115 117 118 55: 240 type=157 (RBDIHS) 116 115 117 119 55: 241 type=158 (RBDIHS) 115 117 119 121 55: 242 type=159 (RBDIHS) 115 117 119 134 55: 243 type=184 (RBDIHS) 117 119 121 124 55: 244 type=185 (RBDIHS) 134 119 121 124 55: 245 type=147 (RBDIHS) 117 119 121 122 55: 246 type=147 (RBDIHS) 117 119 121 123 55: 247 type=148 (RBDIHS) 120 119 121 122 55: 248 type=148 (RBDIHS) 120 119 121 123 55: 249 type=148 (RBDIHS) 120 119 121 124 55: 250 type=149 (RBDIHS) 134 119 121 122 55: 251 type=149 (RBDIHS) 134 119 121 123 55: 252 type=150 (RBDIHS) 117 119 134 136 55: 253 type=151 (RBDIHS) 121 119 134 136 55: 254 type=148 (RBDIHS) 119 121 124 125 55: 255 type=152 (RBDIHS) 119 121 124 126 55: 256 type=152 (RBDIHS) 119 121 124 130 55: 257 type=148 (RBDIHS) 122 121 124 125 55: 258 type=148 (RBDIHS) 122 121 124 126 55: 259 type=148 (RBDIHS) 122 121 124 130 55: 260 type=148 (RBDIHS) 123 121 124 125 55: 261 type=148 (RBDIHS) 123 121 124 126 55: 262 type=148 (RBDIHS) 123 121 124 130 55: 263 type=148 (RBDIHS) 121 124 126 127 55: 264 type=148 (RBDIHS) 121 124 126 128 55: 265 type=148 (RBDIHS) 121 124 126 129 55: 266 type=148 (RBDIHS) 125 124 126 127 55: 267 type=148 (RBDIHS) 125 124 126 128 55: 268 type=148 (RBDIHS) 125 124 126 129 55: 269 type=148 (RBDIHS) 130 124 126 127 55: 270 type=148 (RBDIHS) 130 124 126 128 55: 271 type=148 (RBDIHS) 130 124 126 129 55: 272 type=148 (RBDIHS) 121 124 130 131 55: 273 type=148 (RBDIHS) 121 124 130 132 55: 274 type=148 (RBDIHS) 121 124 130 133 55: 275 type=148 (RBDIHS) 125 124 130 131 55: 276 type=148 (RBDIHS) 125 124 130 132 55: 277 type=148 (RBDIHS) 125 124 130 133 55: 278 type=148 (RBDIHS) 126 124 130 131 55: 279 type=148 (RBDIHS) 126 124 130 132 55: 280 type=148 (RBDIHS) 126 124 130 133 55: 281 type=155 (RBDIHS) 119 134 136 137 55: 282 type=156 (RBDIHS) 119 134 136 138 55: 283 type=155 (RBDIHS) 135 134 136 137 55: 284 type=157 (RBDIHS) 135 134 136 138 55: 285 type=158 (RBDIHS) 134 136 138 140 55: 286 type=159 (RBDIHS) 134 136 138 144 55: 287 type=147 (RBDIHS) 136 138 140 141 55: 288 type=147 (RBDIHS) 136 138 140 142 55: 289 type=147 (RBDIHS) 136 138 140 143 55: 290 type=148 (RBDIHS) 139 138 140 141 55: 291 type=148 (RBDIHS) 139 138 140 142 55: 292 type=148 (RBDIHS) 139 138 140 143 55: 293 type=149 (RBDIHS) 144 138 140 141 55: 294 type=149 (RBDIHS) 144 138 140 142 55: 295 type=149 (RBDIHS) 144 138 140 143 55: 296 type=150 (RBDIHS) 136 138 144 146 55: 297 type=151 (RBDIHS) 140 138 144 146 55: 298 type=155 (RBDIHS) 138 144 146 147 55: 299 type=156 (RBDIHS) 138 144 146 148 55: 300 type=155 (RBDIHS) 145 144 146 147 55: 301 type=157 (RBDIHS) 145 144 146 148 55: 302 type=158 (RBDIHS) 144 146 148 150 55: 303 type=159 (RBDIHS) 144 146 148 154 55: 304 type=147 (RBDIHS) 146 148 150 151 55: 305 type=147 (RBDIHS) 146 148 150 152 55: 306 type=147 (RBDIHS) 146 148 150 153 55: 307 type=148 (RBDIHS) 149 148 150 151 55: 308 type=148 (RBDIHS) 149 148 150 152 55: 309 type=148 (RBDIHS) 149 148 150 153 55: 310 type=149 (RBDIHS) 154 148 150 151 55: 311 type=149 (RBDIHS) 154 148 150 152 55: 312 type=149 (RBDIHS) 154 148 150 153 55: Restr. Dih.: 55: nr: 0 55: CBT Dih.: 55: nr: 0 55: Fourier Dih.: 55: nr: 0 55: Improper Dih.: 55: nr: 0 55: Per. Imp. Dih.: 55: nr: 0 55: Tab. Dih.: 55: nr: 0 55: CMAP Dih.: 55: nr: 0 55: GB 1-2 Pol. (unused): 55: nr: 0 55: GB 1-3 Pol. (unused): 55: nr: 0 55: GB 1-4 Pol. (unused): 55: nr: 0 55: GB Polarization (unused): 55: nr: 0 55: Nonpolar Sol. (unused): 55: nr: 0 55: LJ-14: 55: nr: 1197 55: iatoms: 55: 0 type=186 (LJ14) 0 7 55: 1 type=186 (LJ14) 0 8 55: 2 type=187 (LJ14) 0 9 55: 3 type=188 (LJ14) 0 23 55: 4 type=189 (LJ14) 0 24 55: 5 type=190 (LJ14) 1 5 55: 6 type=190 (LJ14) 1 6 55: 7 type=190 (LJ14) 1 22 55: 8 type=190 (LJ14) 2 5 55: 9 type=190 (LJ14) 2 6 55: 10 type=190 (LJ14) 2 22 55: 11 type=190 (LJ14) 3 5 55: 12 type=190 (LJ14) 3 6 55: 13 type=190 (LJ14) 3 22 55: 14 type=191 (LJ14) 4 10 55: 15 type=191 (LJ14) 4 11 55: 16 type=192 (LJ14) 4 12 55: 17 type=190 (LJ14) 4 25 55: 18 type=192 (LJ14) 4 26 55: 19 type=193 (LJ14) 5 7 55: 20 type=193 (LJ14) 5 8 55: 21 type=191 (LJ14) 5 9 55: 22 type=194 (LJ14) 5 23 55: 23 type=186 (LJ14) 5 24 55: 24 type=191 (LJ14) 6 13 55: 25 type=191 (LJ14) 6 14 55: 26 type=192 (LJ14) 6 15 55: 27 type=195 (LJ14) 6 23 55: 28 type=187 (LJ14) 6 24 55: 29 type=193 (LJ14) 7 10 55: 30 type=193 (LJ14) 7 11 55: 31 type=191 (LJ14) 7 12 55: 32 type=196 (LJ14) 7 22 55: 33 type=193 (LJ14) 8 10 55: 34 type=193 (LJ14) 8 11 55: 35 type=191 (LJ14) 8 12 55: 36 type=196 (LJ14) 8 22 55: 37 type=191 (LJ14) 9 16 55: 38 type=191 (LJ14) 9 17 55: 39 type=187 (LJ14) 9 18 55: 40 type=197 (LJ14) 9 22 55: 41 type=193 (LJ14) 10 13 55: 42 type=193 (LJ14) 10 14 55: 43 type=191 (LJ14) 10 15 55: 44 type=193 (LJ14) 11 13 55: 45 type=193 (LJ14) 11 14 55: 46 type=191 (LJ14) 11 15 55: 47 type=190 (LJ14) 12 19 55: 48 type=190 (LJ14) 12 20 55: 49 type=190 (LJ14) 12 21 55: 50 type=193 (LJ14) 13 16 55: 51 type=193 (LJ14) 13 17 55: 52 type=186 (LJ14) 13 18 55: 53 type=193 (LJ14) 14 16 55: 54 type=193 (LJ14) 14 17 55: 55 type=186 (LJ14) 14 18 55: 56 type=190 (LJ14) 16 19 55: 57 type=190 (LJ14) 16 20 55: 58 type=190 (LJ14) 16 21 55: 59 type=190 (LJ14) 17 19 55: 60 type=190 (LJ14) 17 20 55: 61 type=190 (LJ14) 17 21 55: 62 type=196 (LJ14) 22 27 55: 63 type=197 (LJ14) 22 28 55: 64 type=198 (LJ14) 22 38 55: 65 type=190 (LJ14) 23 25 55: 66 type=195 (LJ14) 23 26 55: 67 type=186 (LJ14) 24 29 55: 68 type=187 (LJ14) 24 30 55: 69 type=187 (LJ14) 24 34 55: 70 type=188 (LJ14) 24 39 55: 71 type=189 (LJ14) 24 40 55: 72 type=190 (LJ14) 25 27 55: 73 type=190 (LJ14) 25 28 55: 74 type=190 (LJ14) 25 38 55: 75 type=191 (LJ14) 26 31 55: 76 type=191 (LJ14) 26 32 55: 77 type=191 (LJ14) 26 33 55: 78 type=191 (LJ14) 26 35 55: 79 type=191 (LJ14) 26 36 55: 80 type=191 (LJ14) 26 37 55: 81 type=190 (LJ14) 26 41 55: 82 type=192 (LJ14) 26 42 55: 83 type=193 (LJ14) 27 29 55: 84 type=191 (LJ14) 27 30 55: 85 type=191 (LJ14) 27 34 55: 86 type=194 (LJ14) 27 39 55: 87 type=186 (LJ14) 27 40 55: 88 type=195 (LJ14) 28 39 55: 89 type=187 (LJ14) 28 40 55: 90 type=193 (LJ14) 29 31 55: 91 type=193 (LJ14) 29 32 55: 92 type=193 (LJ14) 29 33 55: 93 type=193 (LJ14) 29 35 55: 94 type=193 (LJ14) 29 36 55: 95 type=193 (LJ14) 29 37 55: 96 type=196 (LJ14) 29 38 55: 97 type=191 (LJ14) 30 35 55: 98 type=191 (LJ14) 30 36 55: 99 type=191 (LJ14) 30 37 55: 100 type=197 (LJ14) 30 38 55: 101 type=191 (LJ14) 31 34 55: 102 type=191 (LJ14) 32 34 55: 103 type=191 (LJ14) 33 34 55: 104 type=197 (LJ14) 34 38 55: 105 type=196 (LJ14) 38 43 55: 106 type=197 (LJ14) 38 44 55: 107 type=198 (LJ14) 38 58 55: 108 type=190 (LJ14) 39 41 55: 109 type=195 (LJ14) 39 42 55: 110 type=186 (LJ14) 40 45 55: 111 type=186 (LJ14) 40 46 55: 112 type=199 (LJ14) 40 47 55: 113 type=188 (LJ14) 40 59 55: 114 type=189 (LJ14) 40 60 55: 115 type=190 (LJ14) 41 43 55: 116 type=190 (LJ14) 41 44 55: 117 type=190 (LJ14) 41 58 55: 118 type=200 (LJ14) 42 48 55: 119 type=200 (LJ14) 42 50 55: 120 type=190 (LJ14) 42 61 55: 121 type=192 (LJ14) 42 62 55: 122 type=193 (LJ14) 43 45 55: 123 type=193 (LJ14) 43 46 55: 124 type=201 (LJ14) 43 47 55: 125 type=194 (LJ14) 43 59 55: 126 type=186 (LJ14) 43 60 55: 127 type=202 (LJ14) 44 49 55: 128 type=202 (LJ14) 44 51 55: 129 type=200 (LJ14) 44 52 55: 130 type=200 (LJ14) 44 54 55: 131 type=195 (LJ14) 44 59 55: 132 type=187 (LJ14) 44 60 55: 133 type=201 (LJ14) 45 48 55: 134 type=201 (LJ14) 45 50 55: 135 type=196 (LJ14) 45 58 55: 136 type=201 (LJ14) 46 48 55: 137 type=201 (LJ14) 46 50 55: 138 type=196 (LJ14) 46 58 55: 139 type=203 (LJ14) 47 53 55: 140 type=203 (LJ14) 47 55 55: 141 type=204 (LJ14) 47 56 55: 142 type=205 (LJ14) 47 58 55: 143 type=203 (LJ14) 48 51 55: 144 type=204 (LJ14) 48 54 55: 145 type=203 (LJ14) 48 57 55: 146 type=203 (LJ14) 49 50 55: 147 type=206 (LJ14) 49 53 55: 148 type=203 (LJ14) 49 56 55: 149 type=204 (LJ14) 50 52 55: 150 type=203 (LJ14) 50 57 55: 151 type=206 (LJ14) 51 55 55: 152 type=203 (LJ14) 51 56 55: 153 type=203 (LJ14) 52 55 55: 154 type=203 (LJ14) 53 54 55: 155 type=206 (LJ14) 53 57 55: 156 type=206 (LJ14) 55 57 55: 157 type=196 (LJ14) 58 63 55: 158 type=196 (LJ14) 58 64 55: 159 type=198 (LJ14) 58 65 55: 160 type=190 (LJ14) 59 61 55: 161 type=195 (LJ14) 59 62 55: 162 type=188 (LJ14) 60 66 55: 163 type=189 (LJ14) 60 67 55: 164 type=190 (LJ14) 61 63 55: 165 type=190 (LJ14) 61 64 55: 166 type=190 (LJ14) 61 65 55: 167 type=190 (LJ14) 62 68 55: 168 type=192 (LJ14) 62 69 55: 169 type=194 (LJ14) 63 66 55: 170 type=186 (LJ14) 63 67 55: 171 type=194 (LJ14) 64 66 55: 172 type=186 (LJ14) 64 67 55: 173 type=196 (LJ14) 65 70 55: 174 type=197 (LJ14) 65 71 55: 175 type=198 (LJ14) 65 89 55: 176 type=190 (LJ14) 66 68 55: 177 type=195 (LJ14) 66 69 55: 178 type=186 (LJ14) 67 72 55: 179 type=186 (LJ14) 67 73 55: 180 type=187 (LJ14) 67 74 55: 181 type=188 (LJ14) 67 90 55: 182 type=189 (LJ14) 67 91 55: 183 type=190 (LJ14) 68 70 55: 184 type=190 (LJ14) 68 71 55: 185 type=190 (LJ14) 68 89 55: 186 type=191 (LJ14) 69 75 55: 187 type=191 (LJ14) 69 76 55: 188 type=192 (LJ14) 69 77 55: 189 type=190 (LJ14) 69 92 55: 190 type=192 (LJ14) 69 93 55: 191 type=193 (LJ14) 70 72 55: 192 type=193 (LJ14) 70 73 55: 193 type=191 (LJ14) 70 74 55: 194 type=194 (LJ14) 70 90 55: 195 type=186 (LJ14) 70 91 55: 196 type=191 (LJ14) 71 78 55: 197 type=191 (LJ14) 71 79 55: 198 type=187 (LJ14) 71 80 55: 199 type=195 (LJ14) 71 90 55: 200 type=187 (LJ14) 71 91 55: 201 type=193 (LJ14) 72 75 55: 202 type=193 (LJ14) 72 76 55: 203 type=191 (LJ14) 72 77 55: 204 type=196 (LJ14) 72 89 55: 205 type=193 (LJ14) 73 75 55: 206 type=193 (LJ14) 73 76 55: 207 type=191 (LJ14) 73 77 55: 208 type=196 (LJ14) 73 89 55: 209 type=190 (LJ14) 74 81 55: 210 type=207 (LJ14) 74 82 55: 211 type=197 (LJ14) 74 89 55: 212 type=193 (LJ14) 75 78 55: 213 type=193 (LJ14) 75 79 55: 214 type=186 (LJ14) 75 80 55: 215 type=193 (LJ14) 76 78 55: 216 type=193 (LJ14) 76 79 55: 217 type=186 (LJ14) 76 80 55: 218 type=187 (LJ14) 77 83 55: 219 type=187 (LJ14) 77 86 55: 220 type=190 (LJ14) 78 81 55: 221 type=208 (LJ14) 78 82 55: 222 type=190 (LJ14) 79 81 55: 223 type=208 (LJ14) 79 82 55: 224 type=190 (LJ14) 80 84 55: 225 type=190 (LJ14) 80 85 55: 226 type=190 (LJ14) 80 87 55: 227 type=190 (LJ14) 80 88 55: 228 type=190 (LJ14) 81 83 55: 229 type=190 (LJ14) 81 86 55: 230 type=190 (LJ14) 83 87 55: 231 type=190 (LJ14) 83 88 55: 232 type=190 (LJ14) 84 86 55: 233 type=190 (LJ14) 85 86 55: 234 type=196 (LJ14) 89 94 55: 235 type=197 (LJ14) 89 95 55: 236 type=198 (LJ14) 89 100 55: 237 type=190 (LJ14) 90 92 55: 238 type=195 (LJ14) 90 93 55: 239 type=186 (LJ14) 91 96 55: 240 type=186 (LJ14) 91 97 55: 241 type=209 (LJ14) 91 98 55: 242 type=188 (LJ14) 91 101 55: 243 type=189 (LJ14) 91 102 55: 244 type=190 (LJ14) 92 94 55: 245 type=190 (LJ14) 92 95 55: 246 type=190 (LJ14) 92 100 55: 247 type=190 (LJ14) 93 99 55: 248 type=190 (LJ14) 93 103 55: 249 type=192 (LJ14) 93 104 55: 250 type=193 (LJ14) 94 96 55: 251 type=193 (LJ14) 94 97 55: 252 type=210 (LJ14) 94 98 55: 253 type=194 (LJ14) 94 101 55: 254 type=186 (LJ14) 94 102 55: 255 type=195 (LJ14) 95 101 55: 256 type=187 (LJ14) 95 102 55: 257 type=190 (LJ14) 96 99 55: 258 type=196 (LJ14) 96 100 55: 259 type=190 (LJ14) 97 99 55: 260 type=196 (LJ14) 97 100 55: 261 type=211 (LJ14) 98 100 55: 262 type=196 (LJ14) 100 105 55: 263 type=197 (LJ14) 100 106 55: 264 type=198 (LJ14) 100 115 55: 265 type=190 (LJ14) 101 103 55: 266 type=195 (LJ14) 101 104 55: 267 type=186 (LJ14) 102 107 55: 268 type=186 (LJ14) 102 108 55: 269 type=187 (LJ14) 102 109 55: 270 type=188 (LJ14) 102 116 55: 271 type=189 (LJ14) 102 117 55: 272 type=190 (LJ14) 103 105 55: 273 type=190 (LJ14) 103 106 55: 274 type=190 (LJ14) 103 115 55: 275 type=191 (LJ14) 104 110 55: 276 type=191 (LJ14) 104 111 55: 277 type=197 (LJ14) 104 112 55: 278 type=190 (LJ14) 104 118 55: 279 type=192 (LJ14) 104 119 55: 280 type=193 (LJ14) 105 107 55: 281 type=193 (LJ14) 105 108 55: 282 type=191 (LJ14) 105 109 55: 283 type=194 (LJ14) 105 116 55: 284 type=186 (LJ14) 105 117 55: 285 type=195 (LJ14) 106 113 55: 286 type=195 (LJ14) 106 114 55: 287 type=195 (LJ14) 106 116 55: 288 type=187 (LJ14) 106 117 55: 289 type=193 (LJ14) 107 110 55: 290 type=193 (LJ14) 107 111 55: 291 type=196 (LJ14) 107 112 55: 292 type=196 (LJ14) 107 115 55: 293 type=193 (LJ14) 108 110 55: 294 type=193 (LJ14) 108 111 55: 295 type=196 (LJ14) 108 112 55: 296 type=196 (LJ14) 108 115 55: 297 type=197 (LJ14) 109 115 55: 298 type=194 (LJ14) 110 113 55: 299 type=194 (LJ14) 110 114 55: 300 type=194 (LJ14) 111 113 55: 301 type=194 (LJ14) 111 114 55: 302 type=196 (LJ14) 115 120 55: 303 type=197 (LJ14) 115 121 55: 304 type=198 (LJ14) 115 134 55: 305 type=190 (LJ14) 116 118 55: 306 type=195 (LJ14) 116 119 55: 307 type=186 (LJ14) 117 122 55: 308 type=186 (LJ14) 117 123 55: 309 type=187 (LJ14) 117 124 55: 310 type=188 (LJ14) 117 135 55: 311 type=189 (LJ14) 117 136 55: 312 type=190 (LJ14) 118 120 55: 313 type=190 (LJ14) 118 121 55: 314 type=190 (LJ14) 118 134 55: 315 type=191 (LJ14) 119 125 55: 316 type=192 (LJ14) 119 126 55: 317 type=192 (LJ14) 119 130 55: 318 type=190 (LJ14) 119 137 55: 319 type=192 (LJ14) 119 138 55: 320 type=193 (LJ14) 120 122 55: 321 type=193 (LJ14) 120 123 55: 322 type=191 (LJ14) 120 124 55: 323 type=194 (LJ14) 120 135 55: 324 type=186 (LJ14) 120 136 55: 325 type=191 (LJ14) 121 127 55: 326 type=191 (LJ14) 121 128 55: 327 type=191 (LJ14) 121 129 55: 328 type=191 (LJ14) 121 131 55: 329 type=191 (LJ14) 121 132 55: 330 type=191 (LJ14) 121 133 55: 331 type=195 (LJ14) 121 135 55: 332 type=187 (LJ14) 121 136 55: 333 type=193 (LJ14) 122 125 55: 334 type=191 (LJ14) 122 126 55: 335 type=191 (LJ14) 122 130 55: 336 type=196 (LJ14) 122 134 55: 337 type=193 (LJ14) 123 125 55: 338 type=191 (LJ14) 123 126 55: 339 type=191 (LJ14) 123 130 55: 340 type=196 (LJ14) 123 134 55: 341 type=197 (LJ14) 124 134 55: 342 type=193 (LJ14) 125 127 55: 343 type=193 (LJ14) 125 128 55: 344 type=193 (LJ14) 125 129 55: 345 type=193 (LJ14) 125 131 55: 346 type=193 (LJ14) 125 132 55: 347 type=193 (LJ14) 125 133 55: 348 type=191 (LJ14) 126 131 55: 349 type=191 (LJ14) 126 132 55: 350 type=191 (LJ14) 126 133 55: 351 type=191 (LJ14) 127 130 55: 352 type=191 (LJ14) 128 130 55: 353 type=191 (LJ14) 129 130 55: 354 type=196 (LJ14) 134 139 55: 355 type=197 (LJ14) 134 140 55: 356 type=198 (LJ14) 134 144 55: 357 type=190 (LJ14) 135 137 55: 358 type=195 (LJ14) 135 138 55: 359 type=186 (LJ14) 136 141 55: 360 type=186 (LJ14) 136 142 55: 361 type=186 (LJ14) 136 143 55: 362 type=188 (LJ14) 136 145 55: 363 type=189 (LJ14) 136 146 55: 364 type=190 (LJ14) 137 139 55: 365 type=190 (LJ14) 137 140 55: 366 type=190 (LJ14) 137 144 55: 367 type=190 (LJ14) 138 147 55: 368 type=192 (LJ14) 138 148 55: 369 type=193 (LJ14) 139 141 55: 370 type=193 (LJ14) 139 142 55: 371 type=193 (LJ14) 139 143 55: 372 type=194 (LJ14) 139 145 55: 373 type=186 (LJ14) 139 146 55: 374 type=195 (LJ14) 140 145 55: 375 type=187 (LJ14) 140 146 55: 376 type=196 (LJ14) 141 144 55: 377 type=196 (LJ14) 142 144 55: 378 type=196 (LJ14) 143 144 55: 379 type=196 (LJ14) 144 149 55: 380 type=197 (LJ14) 144 150 55: 381 type=198 (LJ14) 144 154 55: 382 type=190 (LJ14) 145 147 55: 383 type=195 (LJ14) 145 148 55: 384 type=186 (LJ14) 146 151 55: 385 type=186 (LJ14) 146 152 55: 386 type=186 (LJ14) 146 153 55: 387 type=188 (LJ14) 146 155 55: 388 type=190 (LJ14) 147 149 55: 389 type=190 (LJ14) 147 150 55: 390 type=190 (LJ14) 147 154 55: 391 type=193 (LJ14) 149 151 55: 392 type=193 (LJ14) 149 152 55: 393 type=193 (LJ14) 149 153 55: 394 type=194 (LJ14) 149 155 55: 395 type=195 (LJ14) 150 155 55: 396 type=196 (LJ14) 151 154 55: 397 type=196 (LJ14) 152 154 55: 398 type=196 (LJ14) 153 154 55: Coulomb-14: 55: nr: 0 55: LJC-14 q: 55: nr: 0 55: LJC Pairs NB: 55: nr: 0 55: LJ (SR): 55: nr: 0 55: Buck.ham (SR): 55: nr: 0 55: LJ (unused): 55: nr: 0 55: B.ham (unused): 55: nr: 0 55: Disper. corr.: 55: nr: 0 55: Coulomb (SR): 55: nr: 0 55: Coul (unused): 55: nr: 0 55: RF excl.: 55: nr: 0 55: Coul. recip.: 55: nr: 0 55: LJ recip.: 55: nr: 0 55: DPD: 55: nr: 0 55: Polarization: 55: nr: 0 55: Water Pol.: 55: nr: 0 55: Thole Pol.: 55: nr: 0 55: Anharm. Pol.: 55: nr: 0 55: Position Rest.: 55: nr: 0 55: Flat-b. P-R.: 55: nr: 0 55: Dis. Rest.: 55: nr: 0 55: D.R.Viol. (nm): 55: nr: 0 55: Orient. Rest.: 55: nr: 0 55: Ori. R. RMSD: 55: nr: 0 55: Angle Rest.: 55: nr: 0 55: Angle Rest. Z: 55: nr: 0 55: Dih. Rest.: 55: nr: 0 55: Dih. Rest. Viol.: 55: nr: 0 55: Constraint: 55: nr: 0 55: Constr. No Conn.: 55: nr: 0 55: Settle: 55: nr: 0 55: Virtual site 1: 55: nr: 0 55: Virtual site 2: 55: nr: 0 55: Virtual site 2fd: 55: nr: 0 55: Virtual site 3: 55: nr: 0 55: Virtual site 3fd: 55: nr: 0 55: Virtual site 3fad: 55: nr: 0 55: Virtual site 3out: 55: nr: 0 55: Virtual site 4fd: 55: nr: 0 55: Virtual site 4fdn: 55: nr: 0 55: Virtual site N: 55: nr: 0 55: COM Pull En.: 55: nr: 0 55: Dens. fitting: 55: nr: 0 55: Quantum En.: 55: nr: 0 55: Potential: 55: nr: 0 55: Kinetic En.: 55: nr: 0 55: Total Energy: 55: nr: 0 55: Conserved En.: 55: nr: 0 55: Temperature: 55: nr: 0 55: Vir. Temp. (not used): 55: nr: 0 55: Pres. DC: 55: nr: 0 55: Pressure: 55: nr: 0 55: dH/dl constr.: 55: nr: 0 55: dVremain/dl: 55: nr: 0 55: dEkin/dl: 55: nr: 0 55: dVcoul/dl: 55: nr: 0 55: dVvdw/dl: 55: nr: 0 55: dVbonded/dl: 55: nr: 0 55: dVrestraint/dl: 55: nr: 0 55: dVtemperature/dl: 55: nr: 0 55: grp[T-Coupling ] nr=1, name=[ rest] 55: grp[Energy Mon. ] nr=1, name=[ rest] 55: grp[Acc. not used] nr=1, name=[ rest] 55: grp[Freeze ] nr=1, name=[ rest] 55: grp[User1 ] nr=1, name=[ rest] 55: grp[User2 ] nr=1, name=[ rest] 55: grp[VCM ] nr=1, name=[ rest] 55: grp[Compressed X] nr=1, name=[ rest] 55: grp[Or. Res. Fit] nr=1, name=[ rest] 55: grp[QMMM ] nr=1, name=[ rest] 55: grpname (11): 55: grpname[0]={name="System"} 55: grpname[1]={name="Protein"} 55: grpname[2]={name="Protein-H"} 55: grpname[3]={name="C-alpha"} 55: grpname[4]={name="Backbone"} 55: grpname[5]={name="MainChain"} 55: grpname[6]={name="MainChain+Cb"} 55: grpname[7]={name="MainChain+H"} 55: grpname[8]={name="SideChain"} 55: grpname[9]={name="SideChain-H"} 55: grpname[10]={name="rest"} 55: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 55: allocated 0 0 0 0 0 0 0 0 0 0 55: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 55: box (3x3): 55: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 55: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 55: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 55: box_rel (3x3): 55: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: boxv (3x3): 55: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: pres_prev (3x3): 55: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: svir_prev (3x3): 55: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: fvir_prev (3x3): 55: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: nosehoover_xi: not available 55: x (156x3): 55: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 55: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 55: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 55: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 55: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 55: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 55: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 55: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 55: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 55: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 55: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 55: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 55: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 55: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 55: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 55: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 55: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 55: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 55: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 55: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 55: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 55: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 55: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 55: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 55: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 55: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 55: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 55: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 55: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 55: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 55: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 55: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 55: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 55: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 55: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 55: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 55: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 55: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 55: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 55: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 55: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 55: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 55: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 55: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 55: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 55: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 55: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 55: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 55: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 55: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 55: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 55: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 55: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 55: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 55: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 55: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 55: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 55: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 55: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 55: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 55: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 55: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 55: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 55: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 55: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 55: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 55: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 55: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 55: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 55: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 55: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 55: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 55: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 55: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 55: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 55: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 55: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 55: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 55: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 55: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 55: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 55: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 55: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 55: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 55: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 55: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 55: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 55: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 55: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 55: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 55: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 55: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 55: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 55: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 55: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 55: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 55: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 55: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 55: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 55: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 55: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 55: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 55: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 55: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 55: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 55: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 55: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 55: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 55: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 55: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 55: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 55: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 55: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 55: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 55: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 55: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 55: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 55: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 55: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 55: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 55: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 55: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 55: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 55: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 55: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 55: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 55: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 55: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 55: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 55: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 55: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 55: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 55: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 55: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 55: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 55: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 55: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 55: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 55: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 55: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 55: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 55: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 55: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 55: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 55: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 55: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 55: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 55: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 55: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 55: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 55: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 55: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 55: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 55: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 55: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 55: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 55: v (156x3): 55: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: Group statistics 55: T-Coupling : 156 (total 156 atoms) 55: Energy Mon. : 156 (total 156 atoms) 55: Acc. not used: 156 (total 156 atoms) 55: Freeze : 156 (total 156 atoms) 55: User1 : 156 (total 156 atoms) 55: User2 : 156 (total 156 atoms) 55: VCM : 156 (total 156 atoms) 55: Compressed X: 156 (total 156 atoms) 55: Or. Res. Fit: 156 (total 156 atoms) 55: QMMM : 156 (total 156 atoms) 55: [ OK ] DumpTest.WorksWithTpr (23 ms) 55: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: [ OK ] DumpTest.WorksWithTprAndMdpWriting (1 ms) 55: [----------] 2 tests from DumpTest (25 ms total) 55: 55: [----------] 3 tests from HelpwritingTest 55: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 55: [ OK ] HelpwritingTest.ConvertTprWritesHelp (4 ms) 55: [ RUN ] HelpwritingTest.DumpWritesHelp 55: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 55: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 55: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (1 ms) 55: [----------] 3 tests from HelpwritingTest (6 ms total) 55: 55: [----------] 4 tests from ReportMethodsTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Setting the LD random seed to -69206017 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 55: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 55: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 55: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 55: [ RUN ] ReportMethodsTest.WritesCorrectInformation 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: [ OK ] ReportMethodsTest.WritesCorrectInformation (5 ms) 55: [ RUN ] ReportMethodsTest.ToolEndToEndTest 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: section: Methods 55: subsection: Simulation system 55: A system of 1 molecules (156 atoms) was simulated. 55: 55: subsection: Simulation settings 55: A total of 0 ns were simulated with a time step of 1 fs. 55: Neighbor searching was performed every 10 steps. 55: The Cut-off algorithm was used for electrostatic interactions. 55: with a cut-off of 1 nm. 55: A single cut-off of 1.1 nm was used for Van der Waals interactions. 55: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 55: [----------] 4 tests from ReportMethodsTest (6 ms total) 55: 55: [----------] 3 tests from ConvertTprTest 55: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Setting the LD random seed to -1083310104 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 0 55: Runtime for the run 0 ps 55: Run end step 0 55: Run end time 0 ps 55: 55: Extending remaining runtime by 100 ps 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 100000 55: Runtime for the run 100 ps 55: Run end step 100000 55: Run end time 100 ps 55: 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 100000 55: Runtime for the run 100 ps 55: Run end step 100000 55: Run end time 100 ps 55: 55: Extending remaining runtime by 100 ps 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 200000 55: Runtime for the run 200 ps 55: Run end step 200000 55: Run end time 200 ps 55: 55: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (476 ms) 55: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Setting the LD random seed to -1275644422 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 0 55: Runtime for the run 0 ps 55: Run end step 0 55: Run end time 0 ps 55: 55: Extending remaining runtime to 100 ps 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 100000 55: Runtime for the run 100 ps 55: Run end step 100000 55: Run end time 100 ps 55: 55: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (463 ms) 55: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Setting nsteps to 102 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Setting the LD random seed to -1191256202 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 0 55: Runtime for the run 0 ps 55: Run end step 0 55: Run end time 0 ps 55: 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 102 55: Runtime for the run 0.102 ps 55: Run end step 102 55: Run end time 0.102 ps 55: 55: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (511 ms) 55: [----------] 3 tests from ConvertTprTest (1452 ms total) 55: 55: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: trr version: GMX_trn_file (single precision) 55: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (7 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (8 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (1 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 55: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (24 ms total) 55: 55: [----------] 30 tests from Works/TrjconvDumpTest 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (13 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (7 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 55: [----------] 30 tests from Works/TrjconvDumpTest (43 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 54 tests from 6 test suites ran. (2832 ms total) 55: [ PASSED ] 54 tests. 55/81 Test #55: ToolUnitTests .................................. Passed 2.88 sec test 56 Start 56: FileIOTests 56: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/FileIOTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/fileio/tests 56: Test timeout computed to be: 30 56: [==========] Running 42 tests from 10 test suites. 56: [----------] Global test environment set-up. 56: [----------] 4 tests from Checkpoint 56: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 56: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 56: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 56: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 56: [ RUN ] Checkpoint.KvtRoundTripInt64 56: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 56: [ RUN ] Checkpoint.KvtRoundTripReal 56: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 56: [----------] 4 tests from Checkpoint (0 ms total) 56: 56: [----------] 2 tests from FileMD5Test 56: [ RUN ] FileMD5Test.CanComputeMD5 56: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 56: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 56: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 56: [----------] 2 tests from FileMD5Test (1 ms total) 56: 56: [----------] 3 tests from MrcSerializer 56: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 56: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 56: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 56: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 56: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 56: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 56: [----------] 3 tests from MrcSerializer (0 ms total) 56: 56: [----------] 4 tests from MrcDensityMap 56: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 56: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 56: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 56: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 56: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 56: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 56: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 56: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (1 ms) 56: [----------] 4 tests from MrcDensityMap (3 ms total) 56: 56: [----------] 8 tests from MrcDensityMapHeaderTest 56: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 56: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 56: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 56: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.IsSane 56: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 56: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 56: 56: [----------] 10 tests from ReadTest 56: [ RUN ] ReadTest.get_eint_ReadsInteger 56: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 56: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side '0.8' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 56: [ RUN ] ReadTest.get_eint_WarnsAboutString 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side 'hello' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 56: [ RUN ] ReadTest.get_eint64_ReadsInteger 56: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 56: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side '0.8' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 56: [ RUN ] ReadTest.get_eint64_WarnsAboutString 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side 'hello' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 56: [ RUN ] ReadTest.get_ereal_ReadsInteger 56: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 56: [ RUN ] ReadTest.get_ereal_ReadsFloat 56: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 56: [ RUN ] ReadTest.get_ereal_WarnsAboutString 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side 'hello' for parameter 'test' in parameter file is not a 56: real value 56: 56: 56: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 56: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 56: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 56: [----------] 10 tests from ReadTest (0 ms total) 56: 56: [----------] 1 test from FileIOXdrSerializerTest 56: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 56: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 56: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 56: 56: [----------] 2 tests from TngTest 56: [ RUN ] TngTest.CanOpenTngFile 56: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 56: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 56: [ OK ] TngTest.CanOpenTngFile (0 ms) 56: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 56: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 56: [----------] 2 tests from TngTest (0 ms total) 56: 56: [----------] 4 tests from XvgioTest 56: [ RUN ] XvgioTest.readXvgIntWorks 56: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 56: [ RUN ] XvgioTest.readXvgRealWorks 56: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 56: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 56: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 56: [ RUN ] XvgioTest.readXvgDeprecatedWorks 56: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 56: [----------] 4 tests from XvgioTest (1 ms total) 56: 56: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (2 ms) 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 56: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (4 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 42 tests from 10 test suites ran. (11 ms total) 56: [ PASSED ] 42 tests. 56/81 Test #56: FileIOTests .................................... Passed 0.03 sec test 57 Start 57: SelectionUnitTests 57: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/SelectionUnitTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/gromacs/selection/tests 57: Test timeout computed to be: 30 57: [==========] Running 201 tests from 11 test suites. 57: [----------] Global test environment set-up. 57: [----------] 1 test from IndexGroupTest 57: [ RUN ] IndexGroupTest.RemovesDuplicates 57: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 57: [----------] 1 test from IndexGroupTest (0 ms total) 57: 57: [----------] 15 tests from IndexBlockTest 57: [ RUN ] IndexBlockTest.CreatesUnknownBlock 57: [ OK ] IndexBlockTest.CreatesUnknownBlock (1 ms) 57: [ RUN ] IndexBlockTest.CreatesAtomBlock 57: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms) 57: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 57: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 57: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 57: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 57: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 57: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (2 ms) 57: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 57: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 57: [ RUN ] IndexBlockTest.CreatesSingleBlock 57: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 57: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 57: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 57: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 57: [----------] 15 tests from IndexBlockTest (8 ms total) 57: 57: [----------] 11 tests from IndexMapTest 57: [ RUN ] IndexMapTest.InitializesAtomBlock 57: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 57: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 57: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 57: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 57: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (1 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 57: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 57: [ RUN ] IndexMapTest.InitializesMoleculeBlock 57: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms) 57: [ RUN ] IndexMapTest.MapsSingleBlock 57: [ OK ] IndexMapTest.MapsSingleBlock (1 ms) 57: [ RUN ] IndexMapTest.MapsResidueBlocks 57: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 57: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 57: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 57: [ RUN ] IndexMapTest.HandlesMultipleRequests 57: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms) 57: [----------] 11 tests from IndexMapTest (8 ms total) 57: 57: [----------] 3 tests from IndexGroupsAndNamesTest 57: [ RUN ] IndexGroupsAndNamesTest.containsNames 57: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 57: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 57: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 57: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 57: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 57: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 57: 57: [----------] 15 tests from NeighborhoodSearchTest 57: [ RUN ] NeighborhoodSearchTest.SimpleSearch 57: [ OK ] NeighborhoodSearchTest.SimpleSearch (33 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 57: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (45 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchBox 57: [ OK ] NeighborhoodSearchTest.GridSearchBox (6 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 57: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (17 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 57: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (10 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 57: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (1 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 57: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (7 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (111 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 57: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 57: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 57: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 57: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 57: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (6 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 57: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 57: [----------] 15 tests from NeighborhoodSearchTest (241 ms total) 57: 57: [----------] 13 tests from PositionCalculationTest 57: [ RUN ] PositionCalculationTest.ComputesAtomPositions 57: [ OK ] PositionCalculationTest.ComputesAtomPositions (4 ms) 57: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 57: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 57: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 57: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (4 ms) 57: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 57: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 57: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (2 ms) 57: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 57: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (1 ms) 57: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 57: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesPositionMask 57: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms) 57: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 57: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 57: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 57: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 57: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 57: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 57: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 57: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms) 57: [----------] 13 tests from PositionCalculationTest (18 ms total) 57: 57: [----------] 33 tests from SelectionCollectionTest 57: [ RUN ] SelectionCollectionTest.HandlesNoSelections 57: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 57: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 57: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 57: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 57: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 57: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 57: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 57: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (14 ms) 57: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 57: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 57: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 57: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 57: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 57: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 57: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 57: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 57: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 57: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 57: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 57: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 57: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 57: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (8 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 57: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 57: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 57: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 57: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 57: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (6 ms) 57: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 57: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 57: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 57: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 57: [----------] 33 tests from SelectionCollectionTest (43 ms total) 57: 57: [----------] 14 tests from SelectionCollectionInteractiveTest 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (4 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 57: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (2 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (1 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 57: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (1 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 57: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 57: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (3 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 57: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 57: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (2 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 57: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 57: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 57: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (1 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 57: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms) 57: [----------] 14 tests from SelectionCollectionInteractiveTest (25 ms total) 57: 57: [----------] 70 tests from SelectionCollectionDataTest 57: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 57: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 57: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (2 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesResnr 57: [ OK ] SelectionCollectionDataTest.HandlesResnr (19 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 57: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 57: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (4 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 57: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 57: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 57: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesChain 57: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMass 57: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesCharge 57: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 57: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 57: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 57: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBeta 57: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesResname 57: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 57: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 57: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (4 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 57: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 57: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (13 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (14 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (4 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (4 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (7 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (8 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 57: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (19 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (1 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 57: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 57: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (37 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 57: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (8 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 57: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 57: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 57: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 57: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 57: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 57: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 57: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (8 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 57: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 57: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 57: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (2 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 57: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 57: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 57: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 57: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 57: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (9 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 57: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (5 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (9 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 57: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 57: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 57: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 57: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 57: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 57: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 57: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (10 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (4 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (6 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (8 ms) 57: [----------] 70 tests from SelectionCollectionDataTest (264 ms total) 57: 57: [----------] 17 tests from SelectionOptionTest 57: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 57: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 57: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 57: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 57: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 57: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (4 ms) 57: [ RUN ] SelectionOptionTest.ChecksEmptySelections 57: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 57: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 57: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooManySelections 57: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 57: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 57: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesAdjuster 57: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 57: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 57: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (4 ms) 57: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 57: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 57: [----------] 17 tests from SelectionOptionTest (15 ms total) 57: 57: [----------] 9 tests from SelectionFileOptionTest 57: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 57: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 57: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 57: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 57: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 57: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 57: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 57: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (8 ms) 57: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 57: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (4 ms) 57: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 57: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 57: [----------] 9 tests from SelectionFileOptionTest (15 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 201 tests from 11 test suites ran. (641 ms total) 57: [ PASSED ] 201 tests. 57/81 Test #57: SelectionUnitTests ............................. Passed 0.69 sec test 58 Start 58: MdrunOutputTests 58: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunOutputTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 58: Test timeout computed to be: 600 58: [==========] Running 12 tests from 5 test suites. 58: [----------] Global test environment set-up. 58: [----------] 1 test from MdrunTest 58: [ RUN ] MdrunTest.WritesHelp 58: [ OK ] MdrunTest.WritesHelp (168 ms) 58: [----------] 1 test from MdrunTest (168 ms total) 58: 58: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 58: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 58: Generating 1-4 interactions: fudge = 0.5 58: Number of degrees of freedom in T-Coupling group rest is 9.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 58: NVE simulation: will use the initial temperature of 2573.591 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 2 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc2' 58: 1 steps, 0.0 ps. 58: Setting the LD random seed to 1329065433 58: 58: Generated 3 of the 3 non-bonded parameter combinations 58: 58: Generated 3 of the 3 1-4 parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.133 0.067 199.7 58: (ns/day) (hour/ns) 58: Performance: 2.586 9.279 58: Reading frame 0 time 0.000 58: # Atoms 6 58: Reading frame 1 time 0.001 Last frame 1 time 0.001 58: 58: 58: Item #frames Timestep (ps) 58: Step 2 0.001 58: Time 2 0.001 58: Lambda 0 58: Coords 2 0.001 58: Velocities 0 58: Forces 0 58: Box 2 0.001 58: Checking file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 58: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (251 ms) 58: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 58: Generating 1-4 interactions: fudge = 0.5 58: Number of degrees of freedom in T-Coupling group rest is 9.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 58: NVE simulation: will use the initial temperature of 2573.591 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 2 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc2' 58: 1 steps, 0.0 ps. 58: Setting the LD random seed to -69369956 58: 58: Generated 3 of the 3 non-bonded parameter combinations 58: 58: Generated 3 of the 3 1-4 parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.003 0.001 188.6 58: (ns/day) (hour/ns) 58: Performance: 127.601 0.188 58: Reading frame 0 time 0.000 58: # Atoms 6 58: Reading frame 1 time 0.001 Last frame 1 time 0.001 58: 58: 58: Item #frames Timestep (ps) 58: Step 2 0.001 58: Time 2 0.001 58: Lambda 0 58: Coords 2 0.001 58: Velocities 0 58: Forces 0 58: Box 2 0.001 58: Checking file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 58: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (30 ms) 58: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 58: Generating 1-4 interactions: fudge = 0.5 58: Number of degrees of freedom in T-Coupling group rest is 9.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 58: NVE simulation: will use the initial temperature of 2573.591 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 2 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc2' 58: 1 steps, 0.0 ps. 58: Setting the LD random seed to -10364931 58: 58: Generated 3 of the 3 non-bonded parameter combinations 58: 58: Generated 3 of the 3 1-4 parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.003 0.002 189.6 58: (ns/day) (hour/ns) 58: Performance: 111.745 0.215 58: Reading frame 0 time 0.000 58: # Atoms 3 58: Reading frame 1 time 0.001 Last frame 1 time 0.001 58: 58: 58: Item #frames Timestep (ps) 58: Step 2 0.001 58: Time 2 0.001 58: Lambda 0 58: Coords 2 0.001 58: Velocities 0 58: Forces 0 58: Box 2 0.001 58: Checking file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 58: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (32 ms) 58: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (314 ms total) 58: 58: [----------] 2 tests from Argon12/OutputFiles 58: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 58: that with the Verlet scheme, nstlist has no effect on the accuracy of 58: your simulation. 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 58: Setting nstcalcenergy (100) equal to nstenergy (4) 58: 58: Number of degrees of freedom in T-Coupling group System is 33.00 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 58: NVE simulation: will use the initial temperature of 68.810 K for 58: determining the Verlet buffer size 58: 58: 58: There were 3 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'Argon' 58: 16 steps, 0.0 ps. 58: Generated 1 of the 1 non-bonded parameter combinations 58: 58: Excluding 1 bonded neighbours molecule type 'Argon' 58: 58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.004 0.002 191.7 58: (ns/day) (hour/ns) 58: Performance: 691.968 0.035 58: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (46 ms) 58: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 58: that with the Verlet scheme, nstlist has no effect on the accuracy of 58: your simulation. 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 58: Setting nstcalcenergy (100) equal to nstenergy (4) 58: 58: Number of degrees of freedom in T-Coupling group System is 33.00 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 58: NVE simulation: will use the initial temperature of 68.810 K for 58: determining the Verlet buffer size 58: 58: 58: There were 3 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'Argon' 58: 16 steps, 0.0 ps. 58: Generated 1 of the 1 non-bonded parameter combinations 58: 58: Excluding 1 bonded neighbours molecule type 'Argon' 58: 58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.042 0.021 199.5 58: (ns/day) (hour/ns) 58: Performance: 69.330 0.346 58: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (47 ms) 58: [----------] 2 tests from Argon12/OutputFiles (94 ms total) 58: 58: [----------] 3 tests from MdrunCanWrite/Trajectories 58: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 6 steps, 0.0 ps. 58: Setting the LD random seed to 2096099709 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.055 0.027 199.2 58: (ns/day) (hour/ns) 58: Performance: 22.052 1.088 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (65 ms) 58: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 6 steps, 0.0 ps. 58: Setting the LD random seed to -1074430241 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.046 0.023 199.2 58: (ns/day) (hour/ns) 58: Performance: 26.071 0.921 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (51 ms) 58: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 6 steps, 0.0 ps. 58: Setting the LD random seed to -1083572761 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.045 0.022 198.9 58: (ns/day) (hour/ns) 58: Performance: 26.899 0.892 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (40 ms) 58: [----------] 3 tests from MdrunCanWrite/Trajectories (157 ms total) 58: 58: [----------] 3 tests from MdrunCanWrite/NptTrajectories 58: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 2 steps, 0.0 ps. 58: Setting the LD random seed to -578830853 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.003 0.002 190.6 58: (ns/day) (hour/ns) 58: Performance: 145.207 0.165 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (54 ms) 58: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 58: 58: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 58: The Berendsen barostat does not generate any strictly correct ensemble, 58: and should not be used for new production simulations (in our opinion). 58: For isotropic scaling we would recommend the C-rescale barostat that also 58: ensures fast relaxation without oscillations, and for anisotropic scaling 58: you likely want to use the Parrinello-Rahman barostat. 58: 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: 58: There was 1 warning 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 2 steps, 0.0 ps. 58: Setting the LD random seed to -2318857 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.115 0.057 199.6 58: (ns/day) (hour/ns) 58: Performance: 4.510 5.321 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (78 ms) 58: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 2 steps, 0.0 ps. 58: Setting the LD random seed to -547358745 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.003 0.002 188.2 58: (ns/day) (hour/ns) 58: Performance: 147.212 0.163 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (57 ms) 58: [----------] 3 tests from MdrunCanWrite/NptTrajectories (190 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 12 tests from 5 test suites ran. (1567 ms total) 58: [ PASSED ] 12 tests. 58/81 Test #58: MdrunOutputTests ............................... Passed 1.63 sec test 59 Start 59: MdrunModulesTests 59: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunModulesTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 59: Test timeout computed to be: 600 59: [==========] Running 15 tests from 3 test suites. 59: [----------] Global test environment set-up. 59: [----------] 9 tests from DensityFittingTest 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -3.8565256e+03 59: Maximum force = 4.5099883e+03 on atom 3 59: Norm of force = 1.6816850e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -562167873 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (302 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -9.8207734e+03 59: Maximum force = 7.3954834e+03 on atom 2 59: Norm of force = 2.7825089e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2115468702 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (224 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 59: 59: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1124:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (21 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Overriding nsteps with value passed on the command line: 4 steps 59: 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 4 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 5 steps. 59: Potential Energy = -1.0954993e+04 59: Maximum force = 7.4724790e+03 on atom 2 59: Norm of force = 2.7758003e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to 1073217327 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (15 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 59: 59: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1124:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (7 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -3.8565256e+03 59: Maximum force = 4.5099883e+03 on atom 3 59: Norm of force = 1.6816850e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -53117971 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (7 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -2.7138664e+04 59: Maximum force = 6.7827656e+03 on atom 2 59: Norm of force = 1.9608866e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1174946821 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (11 ms) 59: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 59: 59: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1124:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 59: Setting the LD random seed to -117619397 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (28 ms) 59: [ RUN ] DensityFittingTest.CheckpointWorks 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 59: Setting nstcalcenergy (100) equal to nstenergy (2) 59: 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 59: NVE simulation: will use the initial temperature of 68.810 K for 59: determining the Verlet buffer size 59: 59: 59: There were 2 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting mdrun 'Argon' 59: 2 steps, 0.0 ps. 59: Setting the LD random seed to -1050504 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 59: 59: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 59: 59: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 59: 59: Note that mdrun will redetermine rlist based on the actual pair-list setup 59: 59: This run will generate roughly 0 Mb of data 59: 59: Writing final coordinates. 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.005 0.008 64.5 59: (ns/day) (hour/ns) 59: Performance: 31.238 0.768 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 59: Can not increase nstlist because an NVE ensemble is used 59: 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting mdrun 'Argon' 59: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 59: 59: Writing final coordinates. 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.003 0.001 191.7 59: (ns/day) (hour/ns) 59: Performance: 302.494 0.079 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (67 ms) 59: [----------] 9 tests from DensityFittingTest (684 ms total) 59: 59: [----------] 4 tests from MimicTest 59: [ RUN ] MimicTest.OneQuantumMol 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 21.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 59: NVE simulation with an initial temperature of zero: will use a Verlet 59: buffer of 10%. Check your energy drift! 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 59: 59: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: NOTE: 47 % of the run time was spent in pair search, 59: you might want to increase nstlist (this has no effect on accuracy) 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.219 0.110 199.9 59: (ns/day) (hour/ns) 59: Performance: 0.788 30.462 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -538050579 59: 59: Generated 10 of the 10 non-bonded parameter combinations 59: 59: Generated 10 of the 10 1-4 parameter combinations 59: 59: Excluding 2 bonded neighbours molecule type 'SOL' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.OneQuantumMol (198 ms) 59: [ RUN ] MimicTest.AllQuantumMol 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 21.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 59: NVE simulation with an initial temperature of zero: will use a Verlet 59: buffer of 10%. Check your energy drift! 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 59: 59: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: NOTE: 14 % of the run time was spent in pair search, 59: you might want to increase nstlist (this has no effect on accuracy) 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.056 0.028 199.7 59: (ns/day) (hour/ns) 59: Performance: 3.084 7.781 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -319860737 59: 59: Generated 10 of the 10 non-bonded parameter combinations 59: 59: Generated 10 of the 10 1-4 parameter combinations 59: 59: Excluding 2 bonded neighbours molecule type 'SOL' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.AllQuantumMol (95 ms) 59: [ RUN ] MimicTest.TwoQuantumMol 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 21.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 59: NVE simulation with an initial temperature of zero: will use a Verlet 59: buffer of 10%. Check your energy drift! 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 59: 59: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.019 0.010 199.2 59: (ns/day) (hour/ns) 59: Performance: 9.063 2.648 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1143086721 59: 59: Generated 10 of the 10 non-bonded parameter combinations 59: 59: Generated 10 of the 10 1-4 parameter combinations 59: 59: Excluding 2 bonded neighbours molecule type 'SOL' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.TwoQuantumMol (20 ms) 59: [ RUN ] MimicTest.BondCuts 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 66.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 59: NVE simulation: will use the initial temperature of 300.368 K for 59: determining the Verlet buffer size 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/ala.gro' 59: 59: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: NOTE: 16 % of the run time was spent in pair search, 59: you might want to increase nstlist (this has no effect on accuracy) 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.001 0.000 192.7 59: (ns/day) (hour/ns) 59: Performance: 178.604 0.134 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1017139857 59: 59: Generated 2211 of the 2211 non-bonded parameter combinations 59: 59: Generated 2211 of the 2211 1-4 parameter combinations 59: 59: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 59: 59: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 59: 59: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 59: 59: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 59: 59: Note that mdrun will redetermine rlist based on the actual pair-list setup 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.BondCuts (34 ms) 59: [----------] 4 tests from MimicTest (349 ms total) 59: 59: [----------] 2 tests from WithIntegrator/ImdTest 59: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 59: Generating 1-4 interactions: fudge = 1 59: 59: NOTE 1 [file glycine_vacuo.top, line 12]: 59: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 59: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 59: the time step of 2.0e-03 ps. 59: Maybe you forgot to change the constraints mdp option. 59: 59: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 59: Number of degrees of freedom in T-Coupling group System is 27.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 2 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34 59: 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: IMD: Enabled. This simulation will accept incoming IMD connections. 59: IMD: Pulling from IMD remote is enabled (-imdpull). 59: IMD: Setting port for connection requests to 0. 59: IMD: Setting up incoming socket. 59: IMD: Listening for IMD connection on port 45797. 59: IMD: -imdwait not set, starting simulation. 59: starting mdrun 'Glycine' 59: 2 steps, 0.0 ps. 59: Setting the LD random seed to -92611073 59: 59: Generated 20503 of the 20503 non-bonded parameter combinations 59: 59: Generated 17396 of the 20503 1-4 parameter combinations 59: 59: Excluding 3 bonded neighbours molecule type 'Glycine' 59: 59: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 59: 59: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 59: 59: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm 59: 59: Note that mdrun will redetermine rlist based on the actual pair-list setup 59: 59: This run will generate roughly 0 Mb of data 59: 59: Writing final coordinates. 59: 59: NOTE: 80 % of the run time was spent in pair search, 59: you might want to increase nstlist (this has no effect on accuracy) 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.013 0.007 197.6 59: (ns/day) (hour/ns) 59: Performance: 78.340 0.306 59: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (306 ms) 59: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 59: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 59: apply to steep. 59: 59: Generating 1-4 interactions: fudge = 1 59: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 59: Number of degrees of freedom in T-Coupling group System is 27.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 2 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: IMD: Enabled. This simulation will accept incoming IMD connections. 59: IMD: Pulling from IMD remote is enabled (-imdpull). 59: IMD: Setting port for connection requests to 0. 59: IMD: Setting up incoming socket. 59: IMD: Listening for IMD connection on port 40727. 59: IMD: -imdwait not set, starting simulation. 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = 1.1977064e+03 59: Maximum force = 1.7794877e+04 on atom 9 59: Norm of force = 7.8732901e+03 59: Setting the LD random seed to 1942450047 59: 59: Generated 20503 of the 20503 non-bonded parameter combinations 59: 59: Generated 17396 of the 20503 1-4 parameter combinations 59: 59: Excluding 3 bonded neighbours molecule type 'Glycine' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (178 ms) 59: [----------] 2 tests from WithIntegrator/ImdTest (484 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 15 tests from 3 test suites ran. (1989 ms total) 59: [ PASSED ] 15 tests. 59/81 Test #59: MdrunModulesTests .............................. Passed 2.04 sec test 60 Start 60: MdrunIOTests 60: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunIOTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 60: Test timeout computed to be: 600 60: [==========] Running 66 tests from 13 test suites. 60: [----------] Global test environment set-up. 60: [----------] 5 tests from GromppTest 60: [ RUN ] GromppTest.EmptyMdpFileWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Setting the LD random seed to -302023300 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.EmptyMdpFileWorks (6 ms) 60: [ RUN ] GromppTest.SimulatedAnnealingWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Simulated annealing for group rest: Periodic, 4 timepoints 60: Time (ps) Temperature (K) 60: 0.0 298.0 60: 2.0 320.0 60: 4.0 320.0 60: 6.0 298.0 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Setting the LD random seed to -621938306 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.SimulatedAnnealingWorks (5 ms) 60: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Simulated annealing for group Methanol: Single, 3 timepoints 60: Time (ps) Temperature (K) 60: 0.0 298.0 60: 3.0 280.0 60: 6.0- 270.0 60: Simulated annealing for group SOL: Periodic, 4 timepoints 60: Time (ps) Temperature (K) 60: 0.0 298.0 60: 2.0 320.0 60: 4.0 320.0 60: 6.0 298.0 60: Number of degrees of freedom in T-Coupling group Methanol is 7.20 60: Number of degrees of freedom in T-Coupling group SOL is 4.80 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Setting the LD random seed to -571049027 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (26 ms) 60: [ RUN ] GromppTest.ValidTransformationCoord 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Pull group 1 'SOL' has 3 atoms 60: Pull group 2 'Methanol' has 3 atoms 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 5 60: 2 3 2 0.613 nm 0.000 nm 60: 1 3 5 60: 2 3 2 0.613 nm 0.000 nm 60: 60: There were 3 notes 60: Setting the LD random seed to -1610769077 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.ValidTransformationCoord (58 ms) 60: [ RUN ] GromppTest.InvalidTransformationCoord 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Pull group 1 'SOL' has 3 atoms 60: Pull group 2 'Methanol' has 3 atoms 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 5 60: 2 3 2 0.613 nm 0.000 nm 60: 1 3 5 60: 2 3 2 Setting the LD random seed to -135266458 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: [ OK ] GromppTest.InvalidTransformationCoord (32 ms) 60: [----------] 5 tests from GromppTest (129 ms total) 60: 60: [----------] 6 tests from MdrunTerminationTest 60: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -1344323973 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 193.9 60: (ns/day) (hour/ns) 60: Performance: 90.900 0.264 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 198.0 60: (ns/day) (hour/ns) 60: Performance: 26.002 0.923 60: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (93 ms) 60: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 1, rlist from 1.024 to 1 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 100 steps, 0.1 ps. 60: 60: Step 2: Run time exceeded 0.000 hours, will terminate the run within 2 steps 60: Setting the LD random seed to -524327 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.5 60: (ns/day) (hour/ns) 60: Performance: 226.280 0.106 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 102 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 102 steps, 0.1 ps (continuing from step 3, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100 60: Runtime for the run 0.1 ps 60: Run end step 100 60: Run end time 0.1 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 102 60: Runtime for the run 0.102 ps 60: Run end step 102 60: Run end time 0.102 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.040 0.020 199.1 60: (ns/day) (hour/ns) 60: Performance: 425.713 0.056 60: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (100 ms) 60: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -321390657 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 188.3 60: (ns/day) (hour/ns) 60: Performance: 220.431 0.109 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 193.0 60: (ns/day) (hour/ns) 60: Performance: 215.964 0.111 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 6 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 6 60: Runtime for the run 0.006 ps 60: Run end step 6 60: Run end time 0.006 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 194.3 60: (ns/day) (hour/ns) 60: Performance: 211.840 0.113 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 8 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 6 60: Runtime for the run 0.006 ps 60: Run end step 6 60: Run end time 0.006 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 8 60: Runtime for the run 0.008 ps 60: Run end step 8 60: Run end time 0.008 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 195.0 60: (ns/day) (hour/ns) 60: Performance: 172.922 0.139 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: NOTE: 55 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.072 0.036 199.6 60: (ns/day) (hour/ns) 60: Performance: 2.383 10.070 60: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (215 ms) 60: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to 658236855 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 187.3 60: (ns/day) (hour/ns) 60: Performance: 198.279 0.121 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps. 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 188.4 60: (ns/day) (hour/ns) 60: Performance: 373.211 0.064 60: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (29 ms) 60: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -19006490 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 188.1 60: (ns/day) (hour/ns) 60: Performance: 211.923 0.113 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 4 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (16 ms) 60: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to 2129554893 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 188.0 60: (ns/day) (hour/ns) 60: Performance: 233.347 0.103 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 193.8 60: (ns/day) (hour/ns) 60: Performance: 228.828 0.105 60: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (23 ms) 60: [----------] 6 tests from MdrunTerminationTest (478 ms total) 60: 60: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 60: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 192.3 60: (ns/day) (hour/ns) 60: Performance: 809.859 0.030 60: trr version: GMX_trn_file (single precision) 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (15 ms) 60: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.014 0.007 198.3 60: (ns/day) (hour/ns) 60: Performance: 204.664 0.117 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (15 ms) 60: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (31 ms total) 60: 60: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.6 60: (ns/day) (hour/ns) 60: Performance: 814.140 0.029 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 187.4 60: (ns/day) (hour/ns) 60: Performance: 495.818 0.048 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 188.9 60: (ns/day) (hour/ns) 60: Performance: 468.336 0.051 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (83 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 198.8 60: (ns/day) (hour/ns) 60: Performance: 146.751 0.164 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.019 0.009 198.7 60: (ns/day) (hour/ns) 60: Performance: 82.218 0.292 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.6 60: (ns/day) (hour/ns) 60: Performance: 372.571 0.064 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (47 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 197.8 60: (ns/day) (hour/ns) 60: Performance: 145.685 0.165 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.010 0.005 196.3 60: (ns/day) (hour/ns) 60: Performance: 150.946 0.159 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.010 0.005 196.3 60: (ns/day) (hour/ns) 60: Performance: 160.105 0.150 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (41 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.7 60: (ns/day) (hour/ns) 60: Performance: 766.338 0.031 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 198.3 60: (ns/day) (hour/ns) 60: Performance: 78.463 0.306 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.8 60: (ns/day) (hour/ns) 60: Performance: 483.399 0.050 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (45 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.4 60: (ns/day) (hour/ns) 60: Performance: 704.390 0.034 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.8 60: (ns/day) (hour/ns) 60: Performance: 480.337 0.050 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.5 60: (ns/day) (hour/ns) 60: Performance: 439.140 0.055 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (48 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.014 0.007 198.4 60: (ns/day) (hour/ns) 60: Performance: 215.157 0.112 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.9 60: (ns/day) (hour/ns) 60: Performance: 371.511 0.065 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 198.4 60: (ns/day) (hour/ns) 60: Performance: 76.219 0.315 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (50 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 193.1 60: (ns/day) (hour/ns) 60: Performance: 704.551 0.034 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.3 60: (ns/day) (hour/ns) 60: Performance: 491.781 0.049 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.1 60: (ns/day) (hour/ns) 60: Performance: 476.547 0.050 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (45 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 189.1 60: (ns/day) (hour/ns) 60: Performance: 687.413 0.035 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 198.4 60: (ns/day) (hour/ns) 60: Performance: 77.645 0.309 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.6 60: (ns/day) (hour/ns) 60: Performance: 424.618 0.057 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (45 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: NOTE: 44 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.018 0.009 197.7 60: (ns/day) (hour/ns) 60: Performance: 161.441 0.149 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 192.7 60: (ns/day) (hour/ns) 60: Performance: 273.960 0.088 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 192.9 60: (ns/day) (hour/ns) 60: Performance: 257.175 0.093 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (91 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 197.8 60: (ns/day) (hour/ns) 60: Performance: 148.663 0.161 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 192.6 60: (ns/day) (hour/ns) 60: Performance: 246.150 0.098 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.023 0.012 198.0 60: (ns/day) (hour/ns) 60: Performance: 65.716 0.365 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (102 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.043 0.022 198.9 60: (ns/day) (hour/ns) 60: Performance: 68.123 0.352 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.025 0.013 197.3 60: (ns/day) (hour/ns) 60: Performance: 60.639 0.396 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.036 0.018 198.7 60: (ns/day) (hour/ns) 60: Performance: 43.039 0.558 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (170 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.031 0.016 198.6 60: (ns/day) (hour/ns) 60: Performance: 94.505 0.254 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.018 0.009 198.1 60: (ns/day) (hour/ns) 60: Performance: 86.950 0.276 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.016 0.008 197.5 60: (ns/day) (hour/ns) 60: Performance: 95.813 0.250 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (170 ms) 60: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (945 ms total) 60: 60: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.018 0.009 196.9 60: (ns/day) (hour/ns) 60: Performance: 162.785 0.147 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.028 0.014 197.7 60: (ns/day) (hour/ns) 60: Performance: 54.229 0.443 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 190.9 60: (ns/day) (hour/ns) 60: Performance: 265.033 0.091 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (260 ms) 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.040 0.020 199.4 60: (ns/day) (hour/ns) 60: Performance: 72.990 0.329 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.016 0.008 198.2 60: (ns/day) (hour/ns) 60: Performance: 97.387 0.246 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 197.4 60: (ns/day) (hour/ns) 60: Performance: 76.536 0.314 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (180 ms) 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.055 0.028 198.5 60: (ns/day) (hour/ns) 60: Performance: 52.546 0.457 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.007 0.003 193.5 60: (ns/day) (hour/ns) 60: Performance: 225.024 0.107 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 192.8 60: (ns/day) (hour/ns) 60: Performance: 271.181 0.089 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (267 ms) 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.055 0.028 199.0 60: (ns/day) (hour/ns) 60: Performance: 53.113 0.452 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.004 155.7 60: (ns/day) (hour/ns) 60: Performance: 195.404 0.123 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.008 0.004 194.4 60: (ns/day) (hour/ns) 60: Performance: 192.896 0.124 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (214 ms) 60: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (923 ms total) 60: 60: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.5 60: (ns/day) (hour/ns) 60: Performance: 752.301 0.032 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.5 60: (ns/day) (hour/ns) 60: Performance: 473.847 0.051 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.1 60: (ns/day) (hour/ns) 60: Performance: 460.013 0.052 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (83 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 193.0 60: (ns/day) (hour/ns) 60: Performance: 707.139 0.034 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 189.6 60: (ns/day) (hour/ns) 60: Performance: 597.452 0.040 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 189.8 60: (ns/day) (hour/ns) 60: Performance: 607.807 0.039 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (47 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 191.6 60: (ns/day) (hour/ns) 60: Performance: 1021.149 0.024 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 190.2 60: (ns/day) (hour/ns) 60: Performance: 616.889 0.039 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 190.3 60: (ns/day) (hour/ns) 60: Performance: 631.582 0.038 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (41 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.021 0.010 199.1 60: (ns/day) (hour/ns) 60: Performance: 142.320 0.169 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 195.2 60: (ns/day) (hour/ns) 60: Performance: 479.208 0.050 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 192.0 60: (ns/day) (hour/ns) 60: Performance: 469.617 0.051 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (43 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.027 0.014 199.3 60: (ns/day) (hour/ns) 60: Performance: 107.053 0.224 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 196.2 60: (ns/day) (hour/ns) 60: Performance: 526.982 0.046 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 193.0 60: (ns/day) (hour/ns) 60: Performance: 504.718 0.048 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (45 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 196.6 60: (ns/day) (hour/ns) 60: Performance: 698.797 0.034 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 195.5 60: (ns/day) (hour/ns) 60: Performance: 443.137 0.054 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 190.7 60: (ns/day) (hour/ns) 60: Performance: 390.691 0.061 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (36 ms) 60: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (297 ms total) 60: 60: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.4 60: (ns/day) (hour/ns) 60: Performance: 706.571 0.034 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.7 60: (ns/day) (hour/ns) 60: Performance: 452.106 0.053 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.4 60: (ns/day) (hour/ns) 60: Performance: 450.544 0.053 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (75 ms) 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 190.8 60: (ns/day) (hour/ns) 60: Performance: 717.767 0.033 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.9 60: (ns/day) (hour/ns) 60: Performance: 462.360 0.052 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: NOTE: 56 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.043 0.022 199.1 60: (ns/day) (hour/ns) 60: Performance: 35.995 0.667 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (111 ms) 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 196.5 60: (ns/day) (hour/ns) 60: Performance: 603.861 0.040 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 198.4 60: (ns/day) (hour/ns) 60: Performance: 75.655 0.317 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.029 0.014 198.9 60: (ns/day) (hour/ns) 60: Performance: 53.838 0.446 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (77 ms) 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 196.7 60: (ns/day) (hour/ns) 60: Performance: 494.231 0.049 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.010 0.005 198.2 60: (ns/day) (hour/ns) 60: Performance: 151.718 0.158 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 193.3 60: (ns/day) (hour/ns) 60: Performance: 456.600 0.053 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (66 ms) 60: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (331 ms total) 60: 60: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.8 60: (ns/day) (hour/ns) 60: Performance: 787.800 0.030 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.0 60: (ns/day) (hour/ns) 60: Performance: 476.966 0.050 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 189.6 60: (ns/day) (hour/ns) 60: Performance: 391.066 0.061 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (123 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 192.9 60: (ns/day) (hour/ns) 60: Performance: 592.308 0.041 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 188.2 60: (ns/day) (hour/ns) 60: Performance: 472.885 0.051 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 182.9 60: (ns/day) (hour/ns) 60: Performance: 429.256 0.056 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (105 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.027 0.013 198.6 60: (ns/day) (hour/ns) 60: Performance: 108.950 0.220 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 190.2 60: (ns/day) (hour/ns) 60: Performance: 544.944 0.044 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.7 60: (ns/day) (hour/ns) 60: Performance: 490.155 0.049 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (75 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.2 60: (ns/day) (hour/ns) 60: Performance: 753.866 0.032 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.0 60: (ns/day) (hour/ns) 60: Performance: 502.851 0.048 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.4 60: (ns/day) (hour/ns) 60: Performance: 360.306 0.067 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (37 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.9 60: (ns/day) (hour/ns) 60: Performance: 775.112 0.031 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 190.0 60: (ns/day) (hour/ns) 60: Performance: 586.283 0.041 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.8 60: (ns/day) (hour/ns) 60: Performance: 477.664 0.050 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (41 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.7 60: (ns/day) (hour/ns) 60: Performance: 757.574 0.032 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 190.8 60: (ns/day) (hour/ns) 60: Performance: 526.387 0.046 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.8 60: (ns/day) (hour/ns) 60: Performance: 507.704 0.047 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (35 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.3 60: (ns/day) (hour/ns) 60: Performance: 782.994 0.031 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 188.6 60: (ns/day) (hour/ns) 60: Performance: 540.698 0.044 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.8 60: (ns/day) (hour/ns) 60: Performance: 476.617 0.050 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (35 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.1 60: (ns/day) (hour/ns) 60: Performance: 764.816 0.031 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 188.5 60: (ns/day) (hour/ns) 60: Performance: 527.920 0.045 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.5 60: (ns/day) (hour/ns) 60: Performance: 424.507 0.057 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (36 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.011 0.006 191.7 60: (ns/day) (hour/ns) 60: Performance: 265.806 0.090 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.9 60: (ns/day) (hour/ns) 60: Performance: 459.300 0.052 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.0 60: (ns/day) (hour/ns) 60: Performance: 507.546 0.047 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (47 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.014 0.007 198.3 60: (ns/day) (hour/ns) 60: Performance: 201.623 0.119 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.009 0.004 197.0 60: (ns/day) (hour/ns) 60: Performance: 174.104 0.138 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.4 60: (ns/day) (hour/ns) 60: Performance: 363.640 0.066 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (52 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 195.9 60: (ns/day) (hour/ns) 60: Performance: 621.403 0.039 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.019 0.009 198.4 60: (ns/day) (hour/ns) 60: Performance: 83.235 0.288 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.012 0.006 196.6 60: (ns/day) (hour/ns) 60: Performance: 124.205 0.193 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (43 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.007 0.004 195.8 60: (ns/day) (hour/ns) 60: Performance: 390.084 0.062 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.3 60: (ns/day) (hour/ns) 60: Performance: 381.952 0.063 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 173.5 60: (ns/day) (hour/ns) 60: Performance: 295.586 0.081 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (38 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.022 0.011 198.9 60: (ns/day) (hour/ns) 60: Performance: 133.664 0.180 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 194.9 60: (ns/day) (hour/ns) 60: Performance: 391.912 0.061 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.1 60: (ns/day) (hour/ns) 60: Performance: 368.613 0.065 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (45 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.007 0.004 195.5 60: (ns/day) (hour/ns) 60: Performance: 386.220 0.062 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 194.8 60: (ns/day) (hour/ns) 60: Performance: 358.327 0.067 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.019 0.010 197.5 60: (ns/day) (hour/ns) 60: Performance: 80.188 0.299 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (42 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 196.0 60: (ns/day) (hour/ns) 60: Performance: 584.718 0.041 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.021 0.011 198.5 60: (ns/day) (hour/ns) 60: Performance: 72.710 0.330 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 190.5 60: (ns/day) (hour/ns) 60: Performance: 344.293 0.070 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (47 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 60: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (0 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 60: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (0 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.022 0.011 199.0 60: (ns/day) (hour/ns) 60: Performance: 132.657 0.181 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.0 60: (ns/day) (hour/ns) 60: Performance: 361.544 0.066 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 192.9 60: (ns/day) (hour/ns) 60: Performance: 304.727 0.079 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (47 ms) 60: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (856 ms total) 60: 60: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 60: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.023 0.012 198.6 60: (ns/day) (hour/ns) 60: Performance: 124.301 0.193 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.022 0.011 198.6 60: (ns/day) (hour/ns) 60: Performance: 71.352 0.336 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 193.0 60: (ns/day) (hour/ns) 60: Performance: 264.367 0.091 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (81 ms) 60: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (81 ms total) 60: 60: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 60: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 191.2 60: (ns/day) (hour/ns) 60: Performance: 591.171 0.041 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 188.0 60: (ns/day) (hour/ns) 60: Performance: 365.433 0.066 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 189.9 60: (ns/day) (hour/ns) 60: Performance: 371.257 0.065 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (95 ms) 60: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: NOTE: 80 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.030 0.015 199.1 60: (ns/day) (hour/ns) 60: Performance: 96.222 0.249 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 194.5 60: (ns/day) (hour/ns) 60: Performance: 319.035 0.075 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 191.5 60: (ns/day) (hour/ns) 60: Performance: 296.904 0.081 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (108 ms) 60: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (204 ms total) 60: 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: Setting the AWH bias MC random seed to -4194535 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Setting the AWH bias MC random seed to 402554794 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 1.443 0.722 200.0 60: (ns/day) (hour/ns) 60: Performance: 2.036 11.790 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.011 0.006 194.4 60: (ns/day) (hour/ns) 60: Performance: 136.825 0.175 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.009 0.005 193.9 60: (ns/day) (hour/ns) 60: Performance: 167.850 0.143 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (876 ms) 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: Setting the AWH bias MC random seed to -757203356 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Setting the AWH bias MC random seed to 1526537825 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.096 0.048 198.8 60: (ns/day) (hour/ns) 60: Performance: 30.526 0.786 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.007 0.008 88.6 60: (ns/day) (hour/ns) 60: Performance: 99.978 0.240 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.047 0.024 198.2 60: (ns/day) (hour/ns) 60: Performance: 32.841 0.731 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (264 ms) 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (1140 ms total) 60: 60: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 60: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.057 0.029 199.5 60: (ns/day) (hour/ns) 60: Performance: 51.209 0.469 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.050 0.025 199.2 60: (ns/day) (hour/ns) 60: Performance: 31.075 0.772 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.024 0.012 196.8 60: (ns/day) (hour/ns) 60: Performance: 62.708 0.383 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (222 ms) 60: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (222 ms total) 60: 60: [----------] 3 tests from Checking/InitialConstraintsTest 60: [ RUN ] Checking/InitialConstraintsTest.Works/0 60: Number of degrees of freedom in T-Coupling group rest is 11.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 1141.954 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc-and-methanol' 60: 1 steps, 0.0 ps. 60: Setting the LD random seed to 1610088446 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 185.8 60: (ns/day) (hour/ns) 60: Performance: 130.215 0.184 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (66 ms) 60: [ RUN ] Checking/InitialConstraintsTest.Works/1 60: Number of degrees of freedom in T-Coupling group rest is 11.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 1141.954 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc-and-methanol' 60: 1 steps, 0.0 ps. 60: Setting the LD random seed to -371210823 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.032 0.016 199.1 60: (ns/day) (hour/ns) 60: Performance: 10.865 2.209 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (55 ms) 60: [ RUN ] Checking/InitialConstraintsTest.Works/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 60: Integrator method md-vv-avek is implemented primarily for validation 60: purposes; for molecular dynamics, you should probably be using md or md-vv 60: 60: Number of degrees of freedom in T-Coupling group rest is 11.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 60: NVE simulation: will use the initial temperature of 1141.954 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc-and-methanol' 60: 1 steps, 0.0 ps. 60: Setting the LD random seed to 1878916853 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 186.4 60: (ns/day) (hour/ns) 60: Performance: 120.515 0.199 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (57 ms) 60: [----------] 3 tests from Checking/InitialConstraintsTest (178 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 66 tests from 13 test suites ran. (7837 ms total) 60: [ PASSED ] 66 tests. 60/81 Test #60: MdrunIOTests ................................... Passed 7.87 sec test 61 Start 61: MdrunTestsOneRank 61: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunTestsOneRank.xml" 61: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 61: Test timeout computed to be: 600 61: [==========] Running 22 tests from 6 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from CompelTest 61: [ RUN ] CompelTest.SwapCanRun 61: Generating 1-4 interactions: fudge = 0.5 61: Split0 group 'Ch0' contains 83 atoms. 61: Split1 group 'Ch1' contains 83 atoms. 61: Solvent group 'SOL' contains 11931 atoms. 61: Swap group 'NA+' contains 19 atoms. 61: Swap group 'CL-' contains 19 atoms. 61: Number of degrees of freedom in T-Coupling group System is 27869.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 61: Removing center of mass motion in the presence of position restraints 61: might cause artifacts. When you are using position restraints to 61: equilibrate a macro-molecule, the artifacts are usually negligible. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: SWAP: Determining initial numbers of ions per compartment. 61: SWAP: Setting pointers for checkpoint writing 61: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 61: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 61: starting mdrun 'Channel_coco in octane membrane' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to -870404 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein' 61: 61: turning all bonds into constraints... 61: 61: Excluding 3 bonded neighbours molecule type 'OCT' 61: 61: turning all bonds into constraints... 61: 61: Excluding 1 bonded neighbours molecule type 'NA' 61: 61: turning all bonds into constraints... 61: 61: Excluding 1 bonded neighbours molecule type 'CL' 61: 61: turning all bonds into constraints... 61: 61: Excluding 3 bonded neighbours molecule type 'Protein' 61: 61: Excluding 3 bonded neighbours molecule type 'OCT' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: turning all bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 1 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 35 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 1.019 0.510 199.9 61: (ns/day) (hour/ns) 61: Performance: 2.543 9.437 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: SWAP: Setting pointers for checkpoint writing 61: SWAP: Copying channel fluxes from checkpoint file data 61: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 61: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 61: starting mdrun 'Channel_coco in octane membrane' 61: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 61: 61: Writing final coordinates. 61: 61: NOTE: 26 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.762 0.381 199.9 61: (ns/day) (hour/ns) 61: Performance: 3.399 7.060 61: [ OK ] CompelTest.SwapCanRun (2025 ms) 61: [----------] 1 test from CompelTest (2025 ms total) 61: 61: [----------] 6 tests from BondedInteractionsTest 61: [ RUN ] BondedInteractionsTest.NormalBondWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 2 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 12 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 190.9 61: (ns/day) (hour/ns) 61: Performance: 187.281 0.128 61: Setting the LD random seed to 1608514861 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.NormalBondWorks (21 ms) 61: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 2 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 17 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 187.0 61: (ns/day) (hour/ns) 61: Performance: 235.930 0.102 61: Setting the LD random seed to -37321025 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.TabulatedBondWorks (39 ms) 61: [ RUN ] BondedInteractionsTest.NormalAngleWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 17 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 187.0 61: (ns/day) (hour/ns) 61: Performance: 222.188 0.108 61: Setting the LD random seed to 1804337151 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.NormalAngleWorks (35 ms) 61: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 16 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 188.8 61: (ns/day) (hour/ns) 61: Performance: 206.607 0.116 61: Setting the LD random seed to -402915354 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (32 ms) 61: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 19 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 186.4 61: (ns/day) (hour/ns) 61: Performance: 270.439 0.089 61: Setting the LD random seed to -289415271 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.NormalDihedralWorks (20 ms) 61: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 17 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 187.4 61: (ns/day) (hour/ns) 61: Performance: 241.914 0.099 61: Setting the LD random seed to -31041 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (27 ms) 61: [----------] 6 tests from BondedInteractionsTest (177 ms total) 61: 61: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to 763280891 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 16 % of the run time was spent in domain decomposition, 61: 0 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.175 0.088 199.7 61: (ns/day) (hour/ns) 61: Performance: 4.923 4.875 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to 1072463790 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.015 0.008 196.4 61: (ns/day) (hour/ns) 61: Performance: 57.434 0.418 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 61: 61: 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (753 ms) 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to -675337345 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.056 0.028 198.9 61: (ns/day) (hour/ns) 61: Performance: 15.339 1.565 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 61: Can not increase nstlist because an NVE ensemble is used 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to 1541924094 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.028 0.014 197.9 61: (ns/day) (hour/ns) 61: Performance: 31.076 0.772 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 61: 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (227 ms) 61: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (981 ms total) 61: 61: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 61: Generating 1-4 interactions: fudge = 0.5 61: Pull group 1 'FirstWaterMolecule' has 3 atoms 61: Pull group 2 'SecondWaterMolecule' has 3 atoms 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: Pull group natoms pbc atom distance at start reference at t=0 61: 1 3 2 61: 2 3 5 1.112 nm 1.000 nm 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to 1744551721 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: turning H bonds into constraints... 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.004 0.002 189.0 61: (ns/day) (hour/ns) 61: Performance: 217.991 0.110 61: Generating 1-4 interactions: fudge = 0.5 61: Pull group 1 'FirstWaterMolecule' has 3 atoms 61: Pull group 2 'SecondWaterMolecule' has 3 atoms 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: Pull group natoms pbc atom distance at start reference at t=0 61: 1 3 2 61: 2 3 5 1.112 nm 1.000 nm 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 61: Can not increase nstlist because an NVE ensemble is used 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to -42467329 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: turning H bonds into constraints... 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.026 0.013 197.8 61: (ns/day) (hour/ns) 61: Performance: 33.059 0.726 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 61: 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (85 ms) 61: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (85 ms total) 61: 61: [----------] 8 tests from FreezeWorks/FreezeGroupTest 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: NVE simulation: will use the initial temperature of 318.937 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 5 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.005 0.002 190.7 61: (ns/day) (hour/ns) 61: Performance: 328.415 0.073 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (63 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: NVE simulation: will use the initial temperature of 318.937 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 5 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.004 0.002 188.8 61: (ns/day) (hour/ns) 61: Performance: 326.770 0.073 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (60 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: NVE simulation: will use the initial temperature of 318.937 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 5 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.005 0.003 192.1 61: (ns/day) (hour/ns) 61: Performance: 302.046 0.079 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (63 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 61: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 61: Parrinello-Rahman is not implemented in md-vv. 61: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (0 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.005 0.003 192.3 61: (ns/day) (hour/ns) 61: Performance: 309.087 0.078 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (80 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.061 0.030 199.1 61: (ns/day) (hour/ns) 61: Performance: 25.500 0.941 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (104 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.044 0.022 198.7 61: (ns/day) (hour/ns) 61: Performance: 34.859 0.688 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (88 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.004 0.002 190.3 61: (ns/day) (hour/ns) 61: Performance: 340.093 0.071 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (78 ms) 61: [----------] 8 tests from FreezeWorks/FreezeGroupTest (539 ms total) 61: 61: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to 1064927231 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.003 0.002 188.2 61: (ns/day) (hour/ns) 61: Performance: 888.327 0.027 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (32 ms) 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because verlet-buffer-tolerance is not set or used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to 1719328245 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 92 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.044 0.022 199.1 61: (ns/day) (hour/ns) 61: Performance: 70.449 0.341 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (39 ms) 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to -67423498 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.004 0.002 191.1 61: (ns/day) (hour/ns) 61: Performance: 840.916 0.029 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (36 ms) 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because verlet-buffer-tolerance is not set or used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to -209723549 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.003 0.002 189.6 61: (ns/day) (hour/ns) 61: Performance: 879.464 0.027 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (32 ms) 61: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (140 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 22 tests from 6 test suites ran. (4953 ms total) 61: [ PASSED ] 21 tests. 61: [ SKIPPED ] 1 test, listed below: 61: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 61/81 Test #61: MdrunTestsOneRank .............................. Passed 5.03 sec test 62 Start 62: MdrunTestsTwoRanks 62: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunTestsTwoRanks.xml" 62: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 62: Test timeout computed to be: 600 62: [==========] Running 22 tests from 6 test suites. 62: [----------] Global test environment set-up. 62: [----------] 1 test from CompelTest 62: [ RUN ] CompelTest.SwapCanRun 62: Generating 1-4 interactions: fudge = 0.5 62: Split0 group 'Ch0' contains 83 atoms. 62: Split1 group 'Ch1' contains 83 atoms. 62: Solvent group 'SOL' contains 11931 atoms. 62: Swap group 'NA+' contains 19 atoms. 62: Swap group 'CL-' contains 19 atoms. 62: Number of degrees of freedom in T-Coupling group System is 27869.00 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 62: Removing center of mass motion in the presence of position restraints 62: might cause artifacts. When you are using position restraints to 62: equilibrate a macro-molecule, the artifacts are usually negligible. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: SWAP: Determining initial numbers of ions per compartment. 62: SWAP: Setting pointers for checkpoint writing 62: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 62: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 62: starting mdrun 'Channel_coco in octane membrane' 62: 2 steps, 0.0 ps. 62: Setting the LD random seed to 929032671 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein' 62: 62: turning all bonds into constraints... 62: 62: Excluding 3 bonded neighbours molecule type 'OCT' 62: 62: turning all bonds into constraints... 62: 62: Excluding 1 bonded neighbours molecule type 'NA' 62: 62: turning all bonds into constraints... 62: 62: Excluding 1 bonded neighbours molecule type 'CL' 62: 62: turning all bonds into constraints... 62: 62: Excluding 3 bonded neighbours molecule type 'Protein' 62: 62: Excluding 3 bonded neighbours molecule type 'OCT' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: turning all bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 1 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 0.4%. 62: The balanceable part of the MD step is 32%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.1%. 62: 62: 62: NOTE: 19 % of the run time was spent in domain decomposition, 62: 13 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 10 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 3.523 0.881 399.9 62: (ns/day) (hour/ns) 62: Performance: 1.471 16.314 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: SWAP: Setting pointers for checkpoint writing 62: SWAP: Copying channel fluxes from checkpoint file data 62: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 62: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 62: starting mdrun 'Channel_coco in octane membrane' 62: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 62: 62: Writing final coordinates. 62: 62: NOTE: 10 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 2.761 0.706 390.8 62: (ns/day) (hour/ns) 62: Performance: 1.834 13.083 62: [ OK ] CompelTest.SwapCanRun (2984 ms) 62: [----------] 1 test from CompelTest (2984 ms total) 62: 62: [----------] 6 tests from BondedInteractionsTest 62: [ RUN ] BondedInteractionsTest.NormalBondWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 2 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 21 % of the run time was spent in domain decomposition, 62: 12 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.002 0.000 375.3 62: (ns/day) (hour/ns) 62: Performance: 177.424 0.135 62: Setting the LD random seed to -254375434 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.NormalBondWorks (77 ms) 62: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 2 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 67 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 13 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.399 0.102 391.9 62: (ns/day) (hour/ns) 62: Performance: 0.848 28.317 62: Setting the LD random seed to -305160457 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.TabulatedBondWorks (238 ms) 62: [ RUN ] BondedInteractionsTest.NormalAngleWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 73 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.384 0.096 399.8 62: (ns/day) (hour/ns) 62: Performance: 0.900 26.656 62: Setting the LD random seed to -43043 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.NormalAngleWorks (239 ms) 62: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 26 % of the run time was spent in domain decomposition, 62: 11 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.002 0.001 375.0 62: (ns/day) (hour/ns) 62: Performance: 171.099 0.140 62: Setting the LD random seed to 2071420923 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (87 ms) 62: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 67 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.385 0.096 399.9 62: (ns/day) (hour/ns) 62: Performance: 0.897 26.746 62: Setting the LD random seed to -27283479 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.NormalDihedralWorks (219 ms) 62: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 15 % of the run time was spent in domain decomposition, 62: 10 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.002 0.001 382.1 62: (ns/day) (hour/ns) 62: Performance: 172.607 0.139 62: Setting the LD random seed to -459347 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (103 ms) 62: [----------] 6 tests from BondedInteractionsTest (968 ms total) 62: 62: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 62: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to -1631748337 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 75 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 10 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.193 0.048 398.6 62: (ns/day) (hour/ns) 62: Performance: 8.923 2.690 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to 2145385305 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 96 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.316 0.079 399.3 62: (ns/day) (hour/ns) 62: Performance: 5.459 4.397 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 62: 62: 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (1401 ms) 62: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to -604029218 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 22 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 6 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 1.536 0.384 399.8 62: (ns/day) (hour/ns) 62: Performance: 1.124 21.345 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 62: Can not increase nstlist because an NVE ensemble is used 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to -287670305 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 33 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 45 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.216 0.056 385.7 62: (ns/day) (hour/ns) 62: Performance: 7.715 3.111 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 62: 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (1151 ms) 62: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (2553 ms total) 62: 62: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 62: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 62: Generating 1-4 interactions: fudge = 0.5 62: Pull group 1 'FirstWaterMolecule' has 3 atoms 62: Pull group 2 'SecondWaterMolecule' has 3 atoms 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: Pull group natoms pbc atom distance at start reference at t=0 62: 1 3 2 62: 2 3 5 1.112 nm 1.000 nm 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to -269619218 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: turning H bonds into constraints... 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 40 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.280 0.070 399.3 62: (ns/day) (hour/ns) 62: Performance: 6.161 3.896 62: Generating 1-4 interactions: fudge = 0.5 62: Pull group 1 'FirstWaterMolecule' has 3 atoms 62: Pull group 2 'SecondWaterMolecule' has 3 atoms 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: Pull group natoms pbc atom distance at start reference at t=0 62: 1 3 2 62: 2 3 5 1.112 nm 1.000 nm 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 62: Can not increase nstlist because an NVE ensemble is used 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to -1552632977 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: turning H bonds into constraints... 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 32 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.009 0.002 378.3 62: (ns/day) (hour/ns) 62: Performance: 187.164 0.128 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 62: 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (372 ms) 62: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (373 ms total) 62: 62: [----------] 8 tests from FreezeWorks/FreezeGroupTest 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: NVE simulation: will use the initial temperature of 318.937 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 11.0%. 62: The balanceable part of the MD step is 2%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.2%. 62: 62: 62: NOTE: 91 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.107 0.027 397.9 62: (ns/day) (hour/ns) 62: Performance: 28.967 0.829 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (264 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: NVE simulation: will use the initial temperature of 318.937 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 15.2%. 62: The balanceable part of the MD step is 49%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 7.4%. 62: 62: NOTE: 7.4 % of the available CPU time was lost due to load imbalance 62: in the domain decomposition. 62: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 62: You can also consider manually changing the decomposition (option -dd); 62: e.g. by using fewer domains along the box dimension in which there is 62: considerable inhomogeneity in the simulated system. 62: 62: NOTE: 11 % of the run time was spent in domain decomposition, 62: 3 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 22 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.011 0.003 381.3 62: (ns/day) (hour/ns) 62: Performance: 276.351 0.087 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (157 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: NVE simulation: will use the initial temperature of 318.937 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 10.4%. 62: The balanceable part of the MD step is 53%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 5.5%. 62: 62: NOTE: 5.5 % of the available CPU time was lost due to load imbalance 62: in the domain decomposition. 62: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 62: You can also consider manually changing the decomposition (option -dd); 62: e.g. by using fewer domains along the box dimension in which there is 62: considerable inhomogeneity in the simulated system. 62: 62: NOTE: 23 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.010 0.003 380.2 62: (ns/day) (hour/ns) 62: Performance: 288.219 0.083 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (105 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 62: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 62: Parrinello-Rahman is not implemented in md-vv. 62: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (0 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 32 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.081 0.026 310.3 62: (ns/day) (hour/ns) 62: Performance: 29.676 0.809 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (92 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 14 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 16 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.693 0.173 399.8 62: (ns/day) (hour/ns) 62: Performance: 4.489 5.347 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (299 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 29 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 12 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.632 0.158 399.7 62: (ns/day) (hour/ns) 62: Performance: 4.921 4.877 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (376 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 78 % of the run time was spent in domain decomposition, 62: 1 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 5 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.041 0.010 395.6 62: (ns/day) (hour/ns) 62: Performance: 74.249 0.323 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (195 ms) 62: [----------] 8 tests from FreezeWorks/FreezeGroupTest (1492 ms total) 62: 62: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to -286261523 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 0.8%. 62: The balanceable part of the MD step is 45%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.4%. 62: 62: 62: NOTE: 14 % of the run time was spent in domain decomposition, 62: 4 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 27 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.009 0.002 378.4 62: (ns/day) (hour/ns) 62: Performance: 675.327 0.036 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (115 ms) 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because verlet-buffer-tolerance is not set or used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to 1053249529 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 1.6%. 62: The balanceable part of the MD step is 57%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.9%. 62: 62: 62: NOTE: 27 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.008 0.002 378.1 62: (ns/day) (hour/ns) 62: Performance: 693.528 0.035 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (47 ms) 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to 1604263931 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 9.6%. 62: The balanceable part of the MD step is 43%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 4.1%. 62: 62: 62: NOTE: 12 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 16 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 1.591 0.398 399.9 62: (ns/day) (hour/ns) 62: Performance: 3.908 6.141 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (522 ms) 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because verlet-buffer-tolerance is not set or used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to 1836046970 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 0.2%. 62: The balanceable part of the MD step is 58%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.1%. 62: 62: 62: NOTE: 26 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.008 0.002 381.4 62: (ns/day) (hour/ns) 62: Performance: 774.885 0.031 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (65 ms) 62: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (751 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 22 tests from 6 test suites ran. (10092 ms total) 62: [ PASSED ] 21 tests. 62: [ SKIPPED ] 1 test, listed below: 62: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 62/81 Test #62: MdrunTestsTwoRanks ............................. Passed 10.15 sec test 63 Start 63: MdrunSingleRankAlgorithmsTests 63: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 63: Test timeout computed to be: 600 63: [==========] Running 4 tests from 2 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from OriresTest 63: [ RUN ] OriresTest.OriresCanRun 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 518.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 note 63: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 63: log). 63: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 63: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 63: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164 63: 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 63: 10 steps, 0.0 ps. 63: Setting the LD random seed to -615035455 63: 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.023 0.012 197.8 63: (ns/day) (hour/ns) 63: Performance: 162.526 0.148 63: [ OK ] OriresTest.OriresCanRun (376 ms) 63: [----------] 1 test from OriresTest (376 ms total) 63: 63: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 63: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 63: Number of degrees of freedom in T-Coupling group rest is 10.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 63: The optimal PME mesh load for parallel simulations is below 0.5 63: and for highly parallel simulations between 0.25 and 0.33, 63: for higher performance, increase the cut-off and the PME grid spacing. 63: 63: 63: 63: There were 2 notes 63: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 63: log). 63: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Dipoles' 63: 20 steps, 0.1 ps. 63: Setting the LD random seed to 167182193 63: 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Dipole' 63: 63: Searching the wall atom type(s) 63: 63: The largest distance between excluded atoms is 0.344 nm 63: Calculating fourier grid dimensions for X Y Z 63: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 63: 63: Estimate for the relative computational load of the PME mesh part: 1.00 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.079 0.040 199.3 63: (ns/day) (hour/ns) 63: Performance: 114.644 0.209 63: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 63: 63: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (1834 ms) 63: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 63: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 63: The supported numbers are > 1. 63: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 63: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: With epsilon_surface > 0 all molecules should be neutral. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: With epsilon_surface > 0 you can only use domain decomposition when there 63: are only small molecules with all bonds constrained (mdrun will check for 63: this). 63: 63: Number of degrees of freedom in T-Coupling group rest is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: The optimal PME mesh load for parallel simulations is below 0.5 63: and for highly parallel simulations between 0.25 and 0.33, 63: for higher performance, increase the cut-off and the PME grid spacing. 63: 63: 63: 63: There were 4 notes 63: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 63: log). 63: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Dipoles' 63: 20 steps, 0.1 ps. 63: Setting the LD random seed to -827986457 63: 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Dipole' 63: 63: The largest distance between excluded atoms is 0.344 nm 63: Calculating fourier grid dimensions for X Y Z 63: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 63: 63: Estimate for the relative computational load of the PME mesh part: 1.00 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.073 0.037 199.4 63: (ns/day) (hour/ns) 63: Performance: 123.547 0.194 63: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 63: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (575 ms) 63: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (2409 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 4 tests from 2 test suites ran. (3102 ms total) 63: [ PASSED ] 4 tests. 63/81 Test #63: MdrunSingleRankAlgorithmsTests ................. Passed 3.14 sec test 64 Start 64: MdrunNonIntegratorTests 64: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 58 tests from 5 test suites. 64: [----------] Global test environment set-up. 64: [----------] 1 test from NonbondedBenchTest 64: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 64: SIMD width: 4 64: System size: 3000 atoms 64: Cut-off radius: 1 nm 64: Number of threads: 1 64: Number of iterations: 1 64: Compute energies: no 64: Ewald excl. corr.: analytical 64: 64: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 64: total useful 64: Ewald all geom. 4xM 20.339 20.3392 0.0585 0.0310 64: [ OK ] NonbondedBenchTest.BasicEndToEndTest (43 ms) 64: [----------] 1 test from NonbondedBenchTest (43 ms total) 64: 64: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -4.7991024e+01 64: Maximum force = 1.8629706e+02 on atom 13 64: Norm of force = 8.7721851e+01 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (742 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 3.02331e+02 on atom 3 64: F-Norm = 1.18024e+02 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -5.5862484e+01 64: Maximum force = 4.2726132e+02 on atom 13 64: Norm of force = 1.8452547e+02 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (778 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 22.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 3.1937714e+02 64: Maximum force = 9.9988643e+03 on atom 9 64: Norm of force = 4.6166996e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (315 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: 64: NOTE 3 [file glycine_vacuo.top, line 12]: 64: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 64: 64: Number of degrees of freedom in T-Coupling group System is 22.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 2.41575e+04 on atom 10 64: F-Norm = 1.18451e+04 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 1.5174426e+02 64: Maximum force = 7.4208862e+03 on atom 9 64: Norm of force = 3.5692992e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (186 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -1.5698444e+02 64: Maximum force = 4.5699695e+02 on atom 17 64: Norm of force = 1.8327127e+02 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (37 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: 64: NOTE 4 [file unknown]: 64: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 1.06802e+03 on atom 28 64: F-Norm = 4.26922e+02 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -1.6941083e+02 64: Maximum force = 2.1829454e+02 on atom 17 64: Norm of force = 7.9205749e+01 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (30 ms) 64: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (2090 ms total) 64: 64: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents converged to Fmax < 10 in 1 steps 64: Potential Energy = -9.7425687e-01 64: Maximum force = 4.0132279e+00 on atom 1 64: Norm of force = 1.6383933e+00 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (32 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 4.01323e+00 on atom 1 64: F-Norm = 1.63839e+00 64: 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 64: Potential Energy = -9.9064195e-01 64: Maximum force = 2.5781672e+00 on atom 1 64: Norm of force = 1.0525324e+00 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (33 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: 64: There was 1 warning 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Low-Memory BFGS Minimizer: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: Using 10 BFGS correction steps. 64: 64: F-max = 4.01323e+00 on atom 1 64: F-Norm = 1.63839e+00 64: 64: 64: writing lowest energy coordinates. 64: 64: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 64: Potential Energy = -9.9064195e-01 64: Maximum force = 2.5781672e+00 on atom 1 64: Norm of force = 1.0525324e+00 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (12 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 3.1939697e+02 64: Maximum force = 9.9704248e+03 on atom 9 64: Norm of force = 4.6227540e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (135 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 2.41672e+04 on atom 10 64: F-Norm = 1.19357e+04 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 1.5625757e+02 64: Maximum force = 7.5018242e+03 on atom 9 64: Norm of force = 3.6139019e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (143 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: 64: There was 1 warning 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Low-Memory BFGS Minimizer: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: Using 10 BFGS correction steps. 64: 64: F-max = 2.41672e+04 on atom 10 64: F-Norm = 1.19357e+04 64: 64: 64: Energy minimization has stopped, but the forces have not converged to the 64: requested precision Fmax < 10 (which may not be possible for your system). It 64: stopped because the algorithm tried to make a new step whose size was too 64: small, or there was no change in the energy since last step. Either way, we 64: regard the minimization as converged to within the available machine 64: precision, given your starting configuration and EM parameters. 64: 64: Double precision normally gives you higher accuracy, but this is often not 64: needed for preparing to run molecular dynamics. 64: 64: writing lowest energy coordinates. 64: 64: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 64: but did not reach the requested Fmax < 10. 64: Potential Energy = 5.6111731e+02 64: Maximum force = 1.2685497e+04 on atom 10 64: Norm of force = 6.0643635e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (145 ms) 64: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (503 ms total) 64: 64: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 192.6 64: (ns/day) (hour/ns) 64: Performance: 755.160 0.032 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 64: 64: trr version: GMX_trn_file (single precision) 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 24 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 193.4 64: (ns/day) (hour/ns) 64: Performance: 1766.732 0.014 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (34 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.014 0.007 198.5 64: (ns/day) (hour/ns) 64: Performance: 210.503 0.114 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 23 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 194.1 64: (ns/day) (hour/ns) 64: Performance: 1729.047 0.014 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (42 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 191.3 64: (ns/day) (hour/ns) 64: Performance: 784.289 0.031 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 25 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 193.3 64: (ns/day) (hour/ns) 64: Performance: 2051.480 0.012 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (41 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 191.1 64: (ns/day) (hour/ns) 64: Performance: 755.530 0.032 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 193.9 64: (ns/day) (hour/ns) 64: Performance: 1941.568 0.012 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (36 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: NVE simulation: will use the initial temperature of 398.997 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 190.8 64: (ns/day) (hour/ns) 64: Performance: 702.542 0.034 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 23 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 193.1 64: (ns/day) (hour/ns) 64: Performance: 1969.499 0.012 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (1044 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: NVE simulation: will use the initial temperature of 398.997 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.006 0.003 194.4 64: (ns/day) (hour/ns) 64: Performance: 508.888 0.047 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 23 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 192.9 64: (ns/day) (hour/ns) 64: Performance: 1945.246 0.012 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (878 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 192.6 64: (ns/day) (hour/ns) 64: Performance: 649.372 0.037 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 91 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.018 0.009 198.9 64: (ns/day) (hour/ns) 64: Performance: 160.061 0.150 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (471 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 193.9 64: (ns/day) (hour/ns) 64: Performance: 661.576 0.036 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 193.6 64: (ns/day) (hour/ns) 64: Performance: 1865.151 0.013 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (742 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: NVE simulation: will use the initial temperature of 456.887 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 6 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.047 0.024 198.8 64: (ns/day) (hour/ns) 64: Performance: 61.917 0.388 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 54 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.075 0.037 199.7 64: (ns/day) (hour/ns) 64: Performance: 39.238 0.612 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (141 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: NVE simulation: will use the initial temperature of 456.887 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 6 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.071 0.036 199.3 64: (ns/day) (hour/ns) 64: Performance: 41.116 0.584 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 86 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.019 0.010 199.0 64: (ns/day) (hour/ns) 64: Performance: 150.497 0.159 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (132 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.055 0.028 199.2 64: (ns/day) (hour/ns) 64: Performance: 53.038 0.453 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.027 0.014 199.3 64: (ns/day) (hour/ns) 64: Performance: 108.762 0.221 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (155 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.006 196.2 64: (ns/day) (hour/ns) 64: Performance: 265.211 0.090 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 17 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 195.0 64: (ns/day) (hour/ns) 64: Performance: 1076.274 0.022 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (95 ms) 64: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (3817 ms total) 64: 64: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.019 0.009 197.5 64: (ns/day) (hour/ns) 64: Performance: 155.241 0.155 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.036 0.018 199.2 64: (ns/day) (hour/ns) 64: Performance: 80.663 0.298 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (85 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.025 0.012 196.9 64: (ns/day) (hour/ns) 64: Performance: 117.798 0.204 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 193.2 64: (ns/day) (hour/ns) 64: Performance: 941.843 0.025 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (109 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.023 0.012 197.2 64: (ns/day) (hour/ns) 64: Performance: 127.633 0.188 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 41 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.002 196.1 64: (ns/day) (hour/ns) 64: Performance: 602.091 0.040 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (88 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.054 0.027 198.9 64: (ns/day) (hour/ns) 64: Performance: 53.647 0.447 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.022 0.011 198.9 64: (ns/day) (hour/ns) 64: Performance: 135.124 0.178 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (108 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.008 0.004 193.8 64: (ns/day) (hour/ns) 64: Performance: 341.005 0.070 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 193.7 64: (ns/day) (hour/ns) 64: Performance: 1002.864 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (64 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.008 0.004 194.5 64: (ns/day) (hour/ns) 64: Performance: 374.778 0.064 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.2 64: (ns/day) (hour/ns) 64: Performance: 939.545 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (42 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.017 0.008 196.8 64: (ns/day) (hour/ns) 64: Performance: 173.172 0.139 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 891.419 0.027 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (44 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.022 0.011 197.0 64: (ns/day) (hour/ns) 64: Performance: 132.591 0.181 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 193.3 64: (ns/day) (hour/ns) 64: Performance: 976.013 0.025 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (55 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.016 0.008 196.1 64: (ns/day) (hour/ns) 64: Performance: 184.521 0.130 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 194.0 64: (ns/day) (hour/ns) 64: Performance: 1014.591 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (45 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.015 0.008 196.0 64: (ns/day) (hour/ns) 64: Performance: 188.064 0.128 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.3 64: (ns/day) (hour/ns) 64: Performance: 947.638 0.025 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (46 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.007 0.004 193.9 64: (ns/day) (hour/ns) 64: Performance: 384.436 0.062 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.8 64: (ns/day) (hour/ns) 64: Performance: 940.980 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (45 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.024 0.012 198.9 64: (ns/day) (hour/ns) 64: Performance: 124.163 0.193 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.3 64: (ns/day) (hour/ns) 64: Performance: 923.074 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (46 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 197.8 64: (ns/day) (hour/ns) 64: Performance: 286.593 0.084 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.2 64: (ns/day) (hour/ns) 64: Performance: 959.594 0.025 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (45 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.017 0.009 198.6 64: (ns/day) (hour/ns) 64: Performance: 171.681 0.140 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 192.1 64: (ns/day) (hour/ns) 64: Performance: 1038.011 0.023 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (44 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.018 0.009 198.6 64: (ns/day) (hour/ns) 64: Performance: 162.031 0.148 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 194.0 64: (ns/day) (hour/ns) 64: Performance: 1012.922 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (47 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.023 0.012 199.0 64: (ns/day) (hour/ns) 64: Performance: 126.069 0.190 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 194.1 64: (ns/day) (hour/ns) 64: Performance: 1058.703 0.023 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (47 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 197.6 64: (ns/day) (hour/ns) 64: Performance: 279.938 0.086 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.5 64: (ns/day) (hour/ns) 64: Performance: 958.549 0.025 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (48 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 197.7 64: (ns/day) (hour/ns) 64: Performance: 290.498 0.083 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 193.8 64: (ns/day) (hour/ns) 64: Performance: 1026.766 0.023 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (48 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 197.7 64: (ns/day) (hour/ns) 64: Performance: 280.371 0.086 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 193.9 64: (ns/day) (hour/ns) 64: Performance: 1014.591 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (46 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.017 0.008 198.6 64: (ns/day) (hour/ns) 64: Performance: 173.148 0.139 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.5 64: (ns/day) (hour/ns) 64: Performance: 961.241 0.025 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (46 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.045 0.023 199.4 64: (ns/day) (hour/ns) 64: Performance: 64.936 0.370 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 17 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.1 64: (ns/day) (hour/ns) 64: Performance: 922.245 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (116 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.034 0.017 199.2 64: (ns/day) (hour/ns) 64: Performance: 85.345 0.281 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 194.4 64: (ns/day) (hour/ns) 64: Performance: 998.475 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (62 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.017 0.008 197.5 64: (ns/day) (hour/ns) 64: Performance: 175.316 0.137 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.028 0.014 199.0 64: (ns/day) (hour/ns) 64: Performance: 102.800 0.233 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (138 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.017 0.008 197.4 64: (ns/day) (hour/ns) 64: Performance: 175.505 0.137 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 48 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.067 0.034 199.6 64: (ns/day) (hour/ns) 64: Performance: 43.611 0.550 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (127 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.015 0.007 196.3 64: (ns/day) (hour/ns) 64: Performance: 197.956 0.121 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 193.9 64: (ns/day) (hour/ns) 64: Performance: 1000.909 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (112 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.025 0.013 198.0 64: (ns/day) (hour/ns) 64: Performance: 116.964 0.205 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.019 0.010 198.6 64: (ns/day) (hour/ns) 64: Performance: 150.291 0.160 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (79 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 194.6 64: (ns/day) (hour/ns) 64: Performance: 316.252 0.076 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 193.8 64: (ns/day) (hour/ns) 64: Performance: 921.693 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (68 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.005 196.1 64: (ns/day) (hour/ns) 64: Performance: 273.173 0.088 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 193.2 64: (ns/day) (hour/ns) 64: Performance: 906.370 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (68 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.024 0.012 197.7 64: (ns/day) (hour/ns) 64: Performance: 120.843 0.199 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.006 197.9 64: (ns/day) (hour/ns) 64: Performance: 257.518 0.093 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (79 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.024 0.012 197.7 64: (ns/day) (hour/ns) 64: Performance: 120.385 0.199 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.0 64: (ns/day) (hour/ns) 64: Performance: 834.882 0.029 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (84 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.006 194.4 64: (ns/day) (hour/ns) 64: Performance: 261.874 0.092 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.0 64: (ns/day) (hour/ns) 64: Performance: 909.716 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (76 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.032 0.016 198.3 64: (ns/day) (hour/ns) 64: Performance: 91.641 0.262 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 193.7 64: (ns/day) (hour/ns) 64: Performance: 877.203 0.027 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (81 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 195.7 64: (ns/day) (hour/ns) 64: Performance: 287.636 0.083 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 190.8 64: (ns/day) (hour/ns) 64: Performance: 917.028 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (66 ms) 64: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (2319 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 58 tests from 5 test suites ran. (9368 ms total) 64: [ PASSED ] 58 tests. 64/81 Test #64: MdrunNonIntegratorTests ........................ Passed 9.43 sec test 65 Start 65: MdrunTpiTests 65: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunTpiTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 2 tests from 1 test suite. 65: [----------] Global test environment set-up. 65: [----------] 2 tests from Simple/TpiTest 65: [ RUN ] Simple/TpiTest.ReproducesOutput/0 65: Ignoring obsolete mdp entry 'ns_type' 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 1308.00 65: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 65: log). 65: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 65: TPI is not implemented for GPUs. 65: 65: Using 1 MPI thread 65: Using 1 OpenMP thread 65: 65: 65: NOTE: Thread affinity was not set. 65: Reading frames from gro file '216 water molecules', 648 atoms. 65: Reading frame 0 time 0.000 mu 3.905e+02 3.905e+02 65: Last frame 0 time 0.000 65: Generated 331705 of the 331705 non-bonded parameter combinations 65: 65: Generated 331705 of the 331705 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Excluding 3 bonded neighbours molecule type 'methane' 65: Analysing residue names: 65: There are: 216 Water residues 65: There are: 1 Other residues 65: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] Simple/TpiTest.ReproducesOutput/0 (799 ms) 65: [ RUN ] Simple/TpiTest.ReproducesOutput/1 65: Ignoring obsolete mdp entry 'ns_type' 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 1308.00 65: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 65: log). 65: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 65: TPI is not implemented for GPUs. 65: 65: Using 1 MPI thread 65: Using 1 OpenMP thread 65: 65: 65: NOTE: Thread affinity was not set. 65: Reading frames from gro file '216 water molecules', 648 atoms. 65: Reading frame 0 time 0.000 mu 1.070e+02 1.070e+02 65: Last frame 0 time 0.000 65: Generated 331705 of the 331705 non-bonded parameter combinations 65: 65: Generated 331705 of the 331705 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Excluding 3 bonded neighbours molecule type 'methane' 65: Analysing residue names: 65: There are: 216 Water residues 65: There are: 1 Other residues 65: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] Simple/TpiTest.ReproducesOutput/1 (504 ms) 65: [----------] 2 tests from Simple/TpiTest (1304 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 2 tests from 1 test suite ran. (1467 ms total) 65: [ PASSED ] 2 tests. 65/81 Test #65: MdrunTpiTests .................................. Passed 1.53 sec test 66 Start 66: MdrunMpiTests 66: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMpiTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 17 tests from 4 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from DomainDecompositionSpecialCasesTest 66: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 0 steps, 0.0 ps. 66: 66: NOTE: 67 % of the run time was spent in domain decomposition, 66: 0 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: NOTE: 6 % of the run time was spent communicating energies, 66: you might want to increase some nst* mdp options 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.377 0.101 374.6 66: (ns/day) (hour/ns) 66: Performance: 0.858 27.981 66: Setting the LD random seed to 1064696760 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (316 ms) 66: [----------] 1 test from DomainDecompositionSpecialCasesTest (316 ms total) 66: 66: [----------] 4 tests from MimicTest 66: [ RUN ] MimicTest.OneQuantumMol 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 21.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 66: 66: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 22 % of the run time was spent in domain decomposition, 66: 10 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 377.6 66: (ns/day) (hour/ns) 66: Performance: 115.484 0.208 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -540029377 66: 66: Generated 10 of the 10 non-bonded parameter combinations 66: 66: Generated 10 of the 10 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MimicTest.OneQuantumMol (162 ms) 66: [ RUN ] MimicTest.AllQuantumMol 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 21.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 66: 66: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 21 % of the run time was spent in domain decomposition, 66: 12 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 378.5 66: (ns/day) (hour/ns) 66: Performance: 140.352 0.171 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -6361137 66: 66: Generated 10 of the 10 non-bonded parameter combinations 66: 66: Generated 10 of the 10 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MimicTest.AllQuantumMol (83 ms) 66: [ RUN ] MimicTest.TwoQuantumMol 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 21.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 66: 66: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 80 % of the run time was spent in domain decomposition, 66: 0 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.241 0.060 399.7 66: (ns/day) (hour/ns) 66: Performance: 1.432 16.763 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1342168215 66: 66: Generated 10 of the 10 non-bonded parameter combinations 66: 66: Generated 10 of the 10 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MimicTest.TwoQuantumMol (281 ms) 66: [ RUN ] MimicTest.BondCuts 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 66.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 66: NVE simulation: will use the initial temperature of 300.368 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/ala.gro' 66: 66: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 45 % of the run time was spent in domain decomposition, 66: 0 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.233 0.058 399.7 66: (ns/day) (hour/ns) 66: Performance: 1.485 16.165 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2038952956 66: 66: Generated 2211 of the 2211 non-bonded parameter combinations 66: 66: Generated 2211 of the 2211 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MimicTest.BondCuts (235 ms) 66: [----------] 4 tests from MimicTest (763 ms total) 66: 66: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -4.7991013e+01 66: Maximum force = 1.8629756e+02 on atom 13 66: Norm of force = 8.7722025e+01 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 66: 66: Generated 330891 of the 330891 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1327 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 3.02331e+02 on atom 3 66: F-Norm = 1.18024e+02 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -5.5862144e+01 66: Maximum force = 4.2727667e+02 on atom 13 66: Norm of force = 1.8453053e+02 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 66: 66: Generated 330891 of the 330891 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (789 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 1 66: Number of degrees of freedom in T-Coupling group System is 22.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 3.1937704e+02 66: Maximum force = 9.9988633e+03 on atom 9 66: Norm of force = 4.6166993e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: turning H bonds into constraints... 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (262 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 1 66: 66: NOTE 3 [file glycine_vacuo.top, line 12]: 66: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 66: 66: Number of degrees of freedom in T-Coupling group System is 22.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 2.41575e+04 on atom 10 66: F-Norm = 1.18451e+04 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 1.5174426e+02 66: Maximum force = 7.4208862e+03 on atom 9 66: Norm of force = 3.5692992e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: turning H bonds into constraints... 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (241 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -1.5698450e+02 66: Maximum force = 4.5699695e+02 on atom 17 66: Norm of force = 1.8326839e+02 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (127 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: 66: NOTE 4 [file unknown]: 66: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 1.06802e+03 on atom 28 66: F-Norm = 4.26922e+02 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -1.6941113e+02 66: Maximum force = 2.1830547e+02 on atom 17 66: Norm of force = 7.9205267e+01 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (195 ms) 66: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (2944 ms total) 66: 66: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents converged to Fmax < 10 in 1 steps 66: Potential Energy = -9.7425687e-01 66: Maximum force = 4.0132279e+00 on atom 3 66: Norm of force = 1.6383933e+00 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (216 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 4.01323e+00 on atom 3 66: F-Norm = 1.63839e+00 66: 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 66: Potential Energy = -9.9064195e-01 66: Maximum force = 2.5781672e+00 on atom 3 66: Norm of force = 1.0525324e+00 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (117 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 notes 66: 66: There was 1 warning 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (5 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 1 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 3.1939685e+02 66: Maximum force = 9.9704248e+03 on atom 9 66: Norm of force = 4.6227568e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (681 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 1 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 2.41672e+04 on atom 10 66: F-Norm = 1.19357e+04 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 1.5625761e+02 66: Maximum force = 7.5018237e+03 on atom 9 66: Norm of force = 3.6139019e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (844 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 66: 66: Generating 1-4 interactions: fudge = 1 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: 66: There was 1 warning 66: Generated 20503 of the 20503 non-bonded parameter combinations 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (298 ms) 66: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (2163 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 17 tests from 4 test suites ran. (6835 ms total) 66: [ PASSED ] 17 tests. 66/81 Test #66: MdrunMpiTests .................................. Passed 6.91 sec test 67 Start 67: MdrunMultiSimTests 67: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMultiSimTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 2 tests from 1 test suite. 67: [----------] Global test environment set-up. 67: [----------] 2 tests from InNvt/MultiSimTerminationTest 67: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 67: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 67: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 67: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 67: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 2 tests from 1 test suite ran. (169 ms total) 67: [ PASSED ] 2 tests. 67: 67: YOU HAVE 4 DISABLED TESTS 67: 67/81 Test #67: MdrunMultiSimTests ............................. Passed 0.23 sec test 68 Start 68: MdrunMultiSimReplexTests 68: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMultiSimReplexTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 1 test from 1 test suite. 68: [----------] Global test environment set-up. 68: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 68: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 68: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 68: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 1 test from 1 test suite ran. (184 ms total) 68: [ PASSED ] 1 test. 68: 68: YOU HAVE 4 DISABLED TESTS 68: 68/81 Test #68: MdrunMultiSimReplexTests ....................... Passed 0.23 sec test 69 Start 69: MdrunMultiSimReplexEquivalenceTests 69: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 0 tests from 0 test suites. 69: [==========] 0 tests from 0 test suites ran. (0 ms total) 69: [ PASSED ] 0 tests. 69: 69: YOU HAVE 10 DISABLED TESTS 69: 69/81 Test #69: MdrunMultiSimReplexEquivalenceTests ............ Passed 0.06 sec test 70 Start 70: MdrunMpi1RankPmeTests 70: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 19 tests from 1 test suite. 70: [----------] Global test environment set-up. 70: [----------] 19 tests from ReproducesEnergies/PmeTest 70: Number of degrees of freedom in T-Coupling group rest is 12.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: NVE simulation: will use the initial temperature of 1046.791 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 2 notes 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Number of degrees of freedom in T-Coupling group rest is 13.00 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: NVE simulation: will use the initial temperature of 966.268 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 notes 70: Setting the LD random seed to -15075521 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: The largest distance between excluded atoms is 0.190 nm 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 70: 70: Estimate for the relative computational load of the PME mesh part: 1.00 70: 70: This run will generate roughly 0 Mb of data 70: Setting the LD random seed to -207701281 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Searching the wall atom type(s) 70: 70: The largest distance between excluded atoms is 0.190 nm 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 70: 70: Estimate for the relative computational load of the PME mesh part: 1.00 70: 70: This run will generate roughly 0 Mb of data 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 70: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc-and-methanol' 70: 20 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.214 0.107 199.8 70: (ns/day) (hour/ns) 70: Performance: 16.920 1.418 70: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (569 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 70: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc-and-methanol' 70: 20 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.157 0.079 199.8 70: (ns/day) (hour/ns) 70: Performance: 23.043 1.042 70: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (106 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 70: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc-and-methanol' 70: 0 steps, 0.0 ps. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.006 0.003 192.0 70: (ns/day) (hour/ns) 70: Performance: 28.289 0.848 70: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (1457 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 70: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc-and-methanol' 70: 20 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.226 0.113 199.8 70: (ns/day) (hour/ns) 70: Performance: 16.043 1.496 70: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (152 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 70: [----------] 19 tests from ReproducesEnergies/PmeTest (2287 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 19 tests from 1 test suite ran. (2478 ms total) 70: [ PASSED ] 4 tests. 70: [ SKIPPED ] 15 tests, listed below: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 70/81 Test #70: MdrunMpi1RankPmeTests .......................... Passed 2.53 sec test 71 Start 71: MdrunMpi2RankPmeTests 71: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 19 tests from 1 test suite. 71: [----------] Global test environment set-up. 71: [----------] 19 tests from ReproducesEnergies/PmeTest 71: Number of degrees of freedom in T-Coupling group rest is 12.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: NVE simulation: will use the initial temperature of 1046.791 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 notes 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Number of degrees of freedom in T-Coupling group rest is 13.00 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: NVE simulation: will use the initial temperature of 966.268 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 3 notes 71: Setting the LD random seed to -335550977 71: 71: Generated 8 of the 10 non-bonded parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'Methanol' 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: The largest distance between excluded atoms is 0.190 nm 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to 803195807 71: 71: Generated 8 of the 10 non-bonded parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'Methanol' 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Searching the wall atom type(s) 71: 71: The largest distance between excluded atoms is 0.190 nm 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was off during the run due to low measured imbalance. 71: Average load imbalance: 8.4%. 71: The balanceable part of the MD step is 1%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 0.1%. 71: 71: 71: NOTE: 11 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.480 0.120 399.4 71: (ns/day) (hour/ns) 71: Performance: 15.101 1.589 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (669 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was off during the run due to low measured imbalance. 71: Average load imbalance: 8.3%. 71: The balanceable part of the MD step is 1%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 0.1%. 71: 71: 71: NOTE: 12 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.688 0.172 399.6 71: (ns/day) (hour/ns) 71: Performance: 10.543 2.276 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (368 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 0 steps, 0.0 ps. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.009 0.002 372.7 71: (ns/day) (hour/ns) 71: Performance: 37.246 0.644 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (995 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 2.491 0.630 395.3 71: (ns/day) (hour/ns) 71: Performance: 2.880 8.335 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (1048 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 11.228 2.808 399.8 71: (ns/day) (hour/ns) 71: Performance: 0.646 37.149 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_auto.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (2945 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 0 steps, 0.0 ps. 71: 71: NOTE: 60 % of the run time was spent in domain decomposition, 71: 14 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.047 0.012 395.7 71: (ns/day) (hour/ns) 71: Performance: 7.307 3.284 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (1077 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was off during the run due to low measured imbalance. 71: Average load imbalance: 8.1%. 71: The balanceable part of the MD step is 1%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 0.1%. 71: 71: 71: NOTE: 12 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.605 0.151 399.6 71: (ns/day) (hour/ns) 71: Performance: 11.985 2.002 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (279 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 71: [----------] 19 tests from ReproducesEnergies/PmeTest (7386 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 19 tests from 1 test suite ran. (7577 ms total) 71: [ PASSED ] 7 tests. 71: [ SKIPPED ] 12 tests, listed below: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 71/81 Test #71: MdrunMpi2RankPmeTests .......................... Passed 7.64 sec test 72 Start 72: MdrunMpiCoordinationBasicTestsOneRank 72: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-mpi-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMpiCoordinationBasicTestsOneRank.xml" 72: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 72: Test timeout computed to be: 1920 72: [==========] Running 1 test from 1 test suite. 72: [----------] Global test environment set-up. 72: [----------] 1 test from BasicPropagators/PeriodicActionsTest 72: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (1) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.019 0.019 99.6 72: (ns/day) (hour/ns) 72: Performance: 75.676 0.317 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (1) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.013 0.013 99.4 72: (ns/day) (hour/ns) 72: Performance: 113.759 0.211 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 5 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.001 0.001 95.7 72: (ns/day) (hour/ns) 72: Performance: 1049.326 0.023 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 4 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 95.7 72: (ns/day) (hour/ns) 72: Performance: 897.784 0.027 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 4 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.003 0.003 97.9 72: (ns/day) (hour/ns) 72: Performance: 432.474 0.055 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 4 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 95.8 72: (ns/day) (hour/ns) 72: Performance: 871.125 0.028 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 72: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (99 ms) 72: [----------] 1 test from BasicPropagators/PeriodicActionsTest (99 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 1 test from 1 test suite ran. (287 ms total) 72: [ PASSED ] 1 test. 72/81 Test #72: MdrunMpiCoordinationBasicTestsOneRank .......... Passed 0.34 sec test 73 Start 73: MdrunMpiCoordinationBasicTestsTwoRanks 73: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-mpi-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMpiCoordinationBasicTestsTwoRanks.xml" 73: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 73: Test timeout computed to be: 1920 73: [==========] Running 1 test from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 1 test from BasicPropagators/PeriodicActionsTest 73: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: Setting nstcalcenergy (100) equal to nstenergy (1) 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: There were 3 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 1.2%. 73: The balanceable part of the MD step is 62%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 0.7%. 73: 73: 73: NOTE: 69 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.046 0.023 198.7 73: (ns/day) (hour/ns) 73: Performance: 63.607 0.377 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: Setting nstcalcenergy (100) equal to nstenergy (1) 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: There were 3 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 0.8%. 73: The balanceable part of the MD step is 61%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 0.5%. 73: 73: 73: NOTE: 26 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.004 0.002 192.1 73: (ns/day) (hour/ns) 73: Performance: 702.462 0.034 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: Setting nstcalcenergy (100) equal to nstenergy (4) 73: 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 5 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was turned on during the run due to measured imbalance. 73: Average load imbalance: 5.8%. 73: The balanceable part of the MD step is 58%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 3.4%. 73: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 73: 73: 73: NOTE: 7 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.017 0.009 197.7 73: (ns/day) (hour/ns) 73: Performance: 171.033 0.140 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 4 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 0.5%. 73: The balanceable part of the MD step is 56%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 0.3%. 73: 73: 73: NOTE: 30 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.004 0.002 190.9 73: (ns/day) (hour/ns) 73: Performance: 671.967 0.036 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 4 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was turned on during the run due to measured imbalance. 73: Average load imbalance: 4.4%. 73: The balanceable part of the MD step is 56%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 2.5%. 73: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 73: 73: 73: NOTE: 30 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.004 0.002 192.4 73: (ns/day) (hour/ns) 73: Performance: 660.264 0.036 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 4 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 0.4%. 73: The balanceable part of the MD step is 59%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 0.2%. 73: 73: 73: NOTE: 30 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.003 0.002 191.5 73: (ns/day) (hour/ns) 73: Performance: 838.062 0.029 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (431 ms) 73: [----------] 1 test from BasicPropagators/PeriodicActionsTest (431 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (590 ms total) 73: [ PASSED ] 1 test. 73/81 Test #73: MdrunMpiCoordinationBasicTestsTwoRanks ......... Passed 0.63 sec test 74 Start 74: MdrunMpiCoordinationCouplingTestsOneRank 74: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-mpi-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMpiCoordinationCouplingTestsOneRank.xml" 74: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 74: Test timeout computed to be: 1920 74: [==========] Running 22 tests from 1 test suite. 74: [----------] Global test environment set-up. 74: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.012 0.012 99.3 74: (ns/day) (hour/ns) 74: Performance: 118.487 0.203 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.4 74: (ns/day) (hour/ns) 74: Performance: 800.077 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.002 94.8 74: (ns/day) (hour/ns) 74: Performance: 931.307 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.3 74: (ns/day) (hour/ns) 74: Performance: 896.086 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.4 74: (ns/day) (hour/ns) 74: Performance: 730.274 0.033 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.7 74: (ns/day) (hour/ns) 74: Performance: 863.675 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (144 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.7 74: (ns/day) (hour/ns) 74: Performance: 595.687 0.040 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.6 74: (ns/day) (hour/ns) 74: Performance: 642.465 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.4 74: (ns/day) (hour/ns) 74: Performance: 844.264 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.004 97.7 74: (ns/day) (hour/ns) 74: Performance: 412.798 0.058 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.5 74: (ns/day) (hour/ns) 74: Performance: 862.104 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.6 74: (ns/day) (hour/ns) 74: Performance: 810.498 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (62 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.5 74: (ns/day) (hour/ns) 74: Performance: 627.224 0.038 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 711.960 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 733.317 0.033 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.4 74: (ns/day) (hour/ns) 74: Performance: 931.870 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.6 74: (ns/day) (hour/ns) 74: Performance: 745.383 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.5 74: (ns/day) (hour/ns) 74: Performance: 771.231 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (60 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.1 74: (ns/day) (hour/ns) 74: Performance: 651.157 0.037 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.4 74: (ns/day) (hour/ns) 74: Performance: 761.413 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 95.5 74: (ns/day) (hour/ns) 74: Performance: 991.087 0.024 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 92.7 74: (ns/day) (hour/ns) 74: Performance: 772.101 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.4 74: (ns/day) (hour/ns) 74: Performance: 648.074 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 19 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.2 74: (ns/day) (hour/ns) 74: Performance: 603.506 0.040 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (63 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 599.688 0.040 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.4 74: (ns/day) (hour/ns) 74: Performance: 862.104 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 848.800 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 885.524 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 928.360 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 863.312 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (59 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.3 74: (ns/day) (hour/ns) 74: Performance: 647.121 0.037 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.6 74: (ns/day) (hour/ns) 74: Performance: 888.334 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.7 74: (ns/day) (hour/ns) 74: Performance: 758.507 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.2 74: (ns/day) (hour/ns) 74: Performance: 773.167 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 808.053 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.3 74: (ns/day) (hour/ns) 74: Performance: 789.213 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (67 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.9 74: (ns/day) (hour/ns) 74: Performance: 614.155 0.039 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 882.480 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 877.078 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 861.019 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.5 74: (ns/day) (hour/ns) 74: Performance: 786.091 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.6 74: (ns/day) (hour/ns) 74: Performance: 831.838 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (56 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.1 74: (ns/day) (hour/ns) 74: Performance: 672.774 0.036 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.6 74: (ns/day) (hour/ns) 74: Performance: 736.033 0.033 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 898.963 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 695.955 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.002 95.2 74: (ns/day) (hour/ns) 74: Performance: 954.539 0.025 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 932.434 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (57 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 651.157 0.037 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 873.471 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.4 74: (ns/day) (hour/ns) 74: Performance: 893.487 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.4 74: (ns/day) (hour/ns) 74: Performance: 901.462 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.010 99.1 74: (ns/day) (hour/ns) 74: Performance: 147.892 0.162 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.3 74: (ns/day) (hour/ns) 74: Performance: 876.454 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (91 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.011 99.2 74: (ns/day) (hour/ns) 74: Performance: 139.794 0.172 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.5 74: (ns/day) (hour/ns) 74: Performance: 881.849 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.010 99.2 74: (ns/day) (hour/ns) 74: Performance: 147.499 0.163 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.5 74: (ns/day) (hour/ns) 74: Performance: 929.901 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 811.352 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.011 0.011 99.1 74: (ns/day) (hour/ns) 74: Performance: 136.399 0.176 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (146 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.006 98.2 74: (ns/day) (hour/ns) 74: Performance: 227.799 0.105 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.010 99.1 74: (ns/day) (hour/ns) 74: Performance: 145.699 0.165 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.002 95.4 74: (ns/day) (hour/ns) 74: Performance: 977.717 0.025 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.5 74: (ns/day) (hour/ns) 74: Performance: 900.277 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.1 74: (ns/day) (hour/ns) 74: Performance: 823.389 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.010 99.0 74: (ns/day) (hour/ns) 74: Performance: 146.814 0.163 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (136 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.006 98.8 74: (ns/day) (hour/ns) 74: Performance: 232.081 0.103 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.8 74: (ns/day) (hour/ns) 74: Performance: 892.064 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.010 99.2 74: (ns/day) (hour/ns) 74: Performance: 153.111 0.157 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 71 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.006 98.9 74: (ns/day) (hour/ns) 74: Performance: 253.179 0.095 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.4 74: (ns/day) (hour/ns) 74: Performance: 890.517 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.010 99.3 74: (ns/day) (hour/ns) 74: Performance: 147.330 0.163 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (134 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.0 74: (ns/day) (hour/ns) 74: Performance: 710.401 0.034 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.6 74: (ns/day) (hour/ns) 74: Performance: 853.623 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 965.156 0.025 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 820.428 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.5 74: (ns/day) (hour/ns) 74: Performance: 810.711 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.010 99.2 74: (ns/day) (hour/ns) 74: Performance: 146.298 0.164 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (136 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.2 74: (ns/day) (hour/ns) 74: Performance: 684.434 0.035 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.006 98.8 74: (ns/day) (hour/ns) 74: Performance: 245.736 0.098 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 949.976 0.025 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.006 98.5 74: (ns/day) (hour/ns) 74: Performance: 244.652 0.098 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 823.609 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.010 99.2 74: (ns/day) (hour/ns) 74: Performance: 147.055 0.163 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (136 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.011 0.012 99.6 74: (ns/day) (hour/ns) 74: Performance: 127.638 0.188 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.4 74: (ns/day) (hour/ns) 74: Performance: 687.183 0.035 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.010 99.6 74: (ns/day) (hour/ns) 74: Performance: 143.828 0.167 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.4 74: (ns/day) (hour/ns) 74: Performance: 670.723 0.036 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.010 0.010 99.6 74: (ns/day) (hour/ns) 74: Performance: 139.950 0.171 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.4 74: (ns/day) (hour/ns) 74: Performance: 699.035 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (146 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: NOTE: 13 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.8 74: (ns/day) (hour/ns) 74: Performance: 447.100 0.054 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.003 98.5 74: (ns/day) (hour/ns) 74: Performance: 584.164 0.041 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.4 74: (ns/day) (hour/ns) 74: Performance: 558.379 0.043 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.007 0.007 99.1 74: (ns/day) (hour/ns) 74: Performance: 222.992 0.108 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.007 99.2 74: (ns/day) (hour/ns) 74: Performance: 225.012 0.107 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.5 74: (ns/day) (hour/ns) 74: Performance: 540.782 0.044 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (90 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.6 74: (ns/day) (hour/ns) 74: Performance: 446.387 0.054 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.7 74: (ns/day) (hour/ns) 74: Performance: 343.706 0.070 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.0 74: (ns/day) (hour/ns) 74: Performance: 538.796 0.045 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.003 98.1 74: (ns/day) (hour/ns) 74: Performance: 581.792 0.041 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.1 74: (ns/day) (hour/ns) 74: Performance: 751.292 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.0 74: (ns/day) (hour/ns) 74: Performance: 652.674 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (69 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 95.9 74: (ns/day) (hour/ns) 74: Performance: 446.355 0.054 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.8 74: (ns/day) (hour/ns) 74: Performance: 592.764 0.040 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.9 74: (ns/day) (hour/ns) 74: Performance: 616.491 0.039 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.1 74: (ns/day) (hour/ns) 74: Performance: 654.964 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.1 74: (ns/day) (hour/ns) 74: Performance: 520.408 0.046 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.1 74: (ns/day) (hour/ns) 74: Performance: 598.872 0.040 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (64 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.1 74: (ns/day) (hour/ns) 74: Performance: 553.264 0.043 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.0 74: (ns/day) (hour/ns) 74: Performance: 553.264 0.043 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.0 74: (ns/day) (hour/ns) 74: Performance: 613.483 0.039 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.9 74: (ns/day) (hour/ns) 74: Performance: 700.227 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.2 74: (ns/day) (hour/ns) 74: Performance: 552.520 0.043 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.2 74: (ns/day) (hour/ns) 74: Performance: 643.001 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (63 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.4 74: (ns/day) (hour/ns) 74: Performance: 430.149 0.056 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.1 74: (ns/day) (hour/ns) 74: Performance: 493.084 0.049 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.3 74: (ns/day) (hour/ns) 74: Performance: 505.879 0.047 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.8 74: (ns/day) (hour/ns) 74: Performance: 532.555 0.045 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.006 99.0 74: (ns/day) (hour/ns) 74: Performance: 228.331 0.105 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.4 74: (ns/day) (hour/ns) 74: Performance: 507.045 0.047 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (72 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.008 0.009 99.0 74: (ns/day) (hour/ns) 74: Performance: 171.705 0.140 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.007 98.8 74: (ns/day) (hour/ns) 74: Performance: 225.151 0.107 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.2 74: (ns/day) (hour/ns) 74: Performance: 437.294 0.055 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.4 74: (ns/day) (hour/ns) 74: Performance: 386.075 0.062 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.3 74: (ns/day) (hour/ns) 74: Performance: 387.240 0.062 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.4 74: (ns/day) (hour/ns) 74: Performance: 393.196 0.061 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (101 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.5 74: (ns/day) (hour/ns) 74: Performance: 400.246 0.060 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.3 74: (ns/day) (hour/ns) 74: Performance: 560.003 0.043 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.0 74: (ns/day) (hour/ns) 74: Performance: 492.257 0.049 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.3 74: (ns/day) (hour/ns) 74: Performance: 527.945 0.045 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.2 74: (ns/day) (hour/ns) 74: Performance: 490.415 0.049 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.3 74: (ns/day) (hour/ns) 74: Performance: 488.587 0.049 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (66 ms) 74: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (2029 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 22 tests from 1 test suite ran. (2207 ms total) 74: [ PASSED ] 22 tests. 74/81 Test #74: MdrunMpiCoordinationCouplingTestsOneRank ....... Passed 2.26 sec test 75 Start 75: MdrunMpiCoordinationCouplingTestsTwoRanks 75: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-mpi-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMpiCoordinationCouplingTestsTwoRanks.xml" 75: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 75: Test timeout computed to be: 1920 75: [==========] Running 22 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.3%. 75: The balanceable part of the MD step is 63%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.2%. 75: 75: 75: NOTE: 70 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.062 0.031 199.0 75: (ns/day) (hour/ns) 75: Performance: 46.939 0.511 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.4%. 75: The balanceable part of the MD step is 60%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.9%. 75: 75: 75: NOTE: 25 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.8 75: (ns/day) (hour/ns) 75: Performance: 670.067 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.5%. 75: The balanceable part of the MD step is 53%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.8%. 75: 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.8 75: (ns/day) (hour/ns) 75: Performance: 788.405 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.1%. 75: The balanceable part of the MD step is 53%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.6%. 75: 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.7 75: (ns/day) (hour/ns) 75: Performance: 694.543 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.5%. 75: The balanceable part of the MD step is 52%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.2%. 75: 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 744.303 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 13.3%. 75: The balanceable part of the MD step is 45%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 5.9%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 5.9 % of the available CPU time was lost due to load imbalance 75: in the domain decomposition. 75: You can consider manually changing the decomposition (option -dd); 75: e.g. by using fewer domains along the box dimension in which there is 75: considerable inhomogeneity in the simulated system. 75: 75: NOTE: 77 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.037 0.019 198.4 75: (ns/day) (hour/ns) 75: Performance: 79.260 0.303 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (428 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.3%. 75: The balanceable part of the MD step is 60%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.8%. 75: 75: 75: NOTE: 70 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.042 0.035 120.1 75: (ns/day) (hour/ns) 75: Performance: 42.215 0.569 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.9%. 75: The balanceable part of the MD step is 58%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.1%. 75: 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.0 75: (ns/day) (hour/ns) 75: Performance: 658.007 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.7%. 75: The balanceable part of the MD step is 58%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.4%. 75: 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 191.8 75: (ns/day) (hour/ns) 75: Performance: 810.444 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.0%. 75: The balanceable part of the MD step is 56%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.1%. 75: 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 192.1 75: (ns/day) (hour/ns) 75: Performance: 596.668 0.040 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.3%. 75: The balanceable part of the MD step is 56%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.7%. 75: 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 192.6 75: (ns/day) (hour/ns) 75: Performance: 595.054 0.040 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.3%. 75: The balanceable part of the MD step is 54%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.7%. 75: 75: 75: NOTE: 6 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.025 0.013 198.2 75: (ns/day) (hour/ns) 75: Performance: 117.288 0.205 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (404 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.6%. 75: The balanceable part of the MD step is 62%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.4%. 75: 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 192.8 75: (ns/day) (hour/ns) 75: Performance: 507.588 0.047 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.7%. 75: The balanceable part of the MD step is 58%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.0%. 75: 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.8 75: (ns/day) (hour/ns) 75: Performance: 651.019 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.7%. 75: The balanceable part of the MD step is 57%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.4%. 75: 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.3 75: (ns/day) (hour/ns) 75: Performance: 678.293 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 4.2%. 75: The balanceable part of the MD step is 54%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.6 75: (ns/day) (hour/ns) 75: Performance: 633.122 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 3.7%. 75: The balanceable part of the MD step is 55%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.1%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.6 75: (ns/day) (hour/ns) 75: Performance: 701.263 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.0%. 75: The balanceable part of the MD step is 54%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.1%. 75: 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.2 75: (ns/day) (hour/ns) 75: Performance: 632.537 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (272 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 192.3 75: (ns/day) (hour/ns) 75: Performance: 570.875 0.042 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.6 75: (ns/day) (hour/ns) 75: Performance: 718.437 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.5 75: (ns/day) (hour/ns) 75: Performance: 777.902 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.8 75: (ns/day) (hour/ns) 75: Performance: 708.318 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.3 75: (ns/day) (hour/ns) 75: Performance: 775.893 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.2 75: (ns/day) (hour/ns) 75: Performance: 797.539 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (355 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 25 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 192.0 75: (ns/day) (hour/ns) 75: Performance: 559.952 0.043 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.4 75: (ns/day) (hour/ns) 75: Performance: 683.713 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 189.0 75: (ns/day) (hour/ns) 75: Performance: 811.779 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.3 75: (ns/day) (hour/ns) 75: Performance: 700.864 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.5 75: (ns/day) (hour/ns) 75: Performance: 620.683 0.039 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.1 75: (ns/day) (hour/ns) 75: Performance: 695.484 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (368 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 23 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 193.4 75: (ns/day) (hour/ns) 75: Performance: 677.845 0.035 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.1 75: (ns/day) (hour/ns) 75: Performance: 650.538 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 190.8 75: (ns/day) (hour/ns) 75: Performance: 916.414 0.026 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 190.6 75: (ns/day) (hour/ns) 75: Performance: 867.079 0.028 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 191.2 75: (ns/day) (hour/ns) 75: Performance: 898.111 0.027 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.7 75: (ns/day) (hour/ns) 75: Performance: 675.430 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (300 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 87 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.034 0.023 147.9 75: (ns/day) (hour/ns) 75: Performance: 64.216 0.374 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.0 75: (ns/day) (hour/ns) 75: Performance: 686.035 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 59 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.980 0.514 190.7 75: (ns/day) (hour/ns) 75: Performance: 2.858 8.398 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.2 75: (ns/day) (hour/ns) 75: Performance: 624.363 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.0 75: (ns/day) (hour/ns) 75: Performance: 685.729 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.3 75: (ns/day) (hour/ns) 75: Performance: 706.612 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1426 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 192.2 75: (ns/day) (hour/ns) 75: Performance: 549.955 0.044 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.2 75: (ns/day) (hour/ns) 75: Performance: 674.986 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 15 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.005 133.8 75: (ns/day) (hour/ns) 75: Performance: 290.532 0.083 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 41 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.004 194.5 75: (ns/day) (hour/ns) 75: Performance: 364.640 0.066 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 190.6 75: (ns/day) (hour/ns) 75: Performance: 619.809 0.039 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 190.8 75: (ns/day) (hour/ns) 75: Performance: 820.483 0.029 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (427 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 63 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.012 0.006 194.5 75: (ns/day) (hour/ns) 75: Performance: 229.492 0.105 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.5 75: (ns/day) (hour/ns) 75: Performance: 668.358 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.6 75: (ns/day) (hour/ns) 75: Performance: 689.644 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.0 75: (ns/day) (hour/ns) 75: Performance: 672.591 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.8 75: (ns/day) (hour/ns) 75: Performance: 665.686 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.5 75: (ns/day) (hour/ns) 75: Performance: 667.996 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (208 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 191.3 75: (ns/day) (hour/ns) 75: Performance: 561.560 0.043 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 60 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.023 0.012 198.1 75: (ns/day) (hour/ns) 75: Performance: 127.087 0.189 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 188.3 75: (ns/day) (hour/ns) 75: Performance: 812.636 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.0 75: (ns/day) (hour/ns) 75: Performance: 710.605 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.0 75: (ns/day) (hour/ns) 75: Performance: 714.686 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.3 75: (ns/day) (hour/ns) 75: Performance: 751.934 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (616 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 24 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 192.4 75: (ns/day) (hour/ns) 75: Performance: 537.082 0.045 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.6 75: (ns/day) (hour/ns) 75: Performance: 711.015 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.8 75: (ns/day) (hour/ns) 75: Performance: 751.888 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 11 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.018 21.2 75: (ns/day) (hour/ns) 75: Performance: 81.460 0.295 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.7 75: (ns/day) (hour/ns) 75: Performance: 626.969 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 188.4 75: (ns/day) (hour/ns) 75: Performance: 672.444 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (327 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 24 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.017 33.1 75: (ns/day) (hour/ns) 75: Performance: 86.950 0.276 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 190.4 75: (ns/day) (hour/ns) 75: Performance: 613.941 0.039 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.3 75: (ns/day) (hour/ns) 75: Performance: 799.091 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 192.7 75: (ns/day) (hour/ns) 75: Performance: 937.543 0.026 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.0 75: (ns/day) (hour/ns) 75: Performance: 643.572 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.1 75: (ns/day) (hour/ns) 75: Performance: 736.033 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (369 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 192.1 75: (ns/day) (hour/ns) 75: Performance: 579.303 0.041 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.8 75: (ns/day) (hour/ns) 75: Performance: 722.947 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.0 75: (ns/day) (hour/ns) 75: Performance: 765.624 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.1 75: (ns/day) (hour/ns) 75: Performance: 658.394 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.5 75: (ns/day) (hour/ns) 75: Performance: 691.463 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.5 75: (ns/day) (hour/ns) 75: Performance: 720.832 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (358 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 24 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 193.7 75: (ns/day) (hour/ns) 75: Performance: 529.579 0.045 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.0 75: (ns/day) (hour/ns) 75: Performance: 662.679 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.1 75: (ns/day) (hour/ns) 75: Performance: 775.210 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.2 75: (ns/day) (hour/ns) 75: Performance: 717.474 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.8 75: (ns/day) (hour/ns) 75: Performance: 648.962 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.8 75: (ns/day) (hour/ns) 75: Performance: 744.078 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (339 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.7%. 75: The balanceable part of the MD step is 67%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.5%. 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.015 41.9 75: (ns/day) (hour/ns) 75: Performance: 95.574 0.251 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.9%. 75: The balanceable part of the MD step is 67%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.6%. 75: 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 190.6 75: (ns/day) (hour/ns) 75: Performance: 520.452 0.046 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 85.4%. 75: The balanceable part of the MD step is 26%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 22.3%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 22.3 % of the available CPU time was lost due to load imbalance 75: in the domain decomposition. 75: You can consider manually changing the decomposition (option -dd); 75: e.g. by using fewer domains along the box dimension in which there is 75: considerable inhomogeneity in the simulated system. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.053 0.027 199.0 75: (ns/day) (hour/ns) 75: Performance: 55.267 0.434 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.0%. 75: The balanceable part of the MD step is 64%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.3%. 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 192.4 75: (ns/day) (hour/ns) 75: Performance: 589.023 0.041 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.8%. 75: The balanceable part of the MD step is 61%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.7%. 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 191.6 75: (ns/day) (hour/ns) 75: Performance: 469.504 0.051 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.4%. 75: The balanceable part of the MD step is 62%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.3%. 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 191.5 75: (ns/day) (hour/ns) 75: Performance: 479.890 0.050 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (536 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.3%. 75: The balanceable part of the MD step is 64%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.2%. 75: 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.004 193.6 75: (ns/day) (hour/ns) 75: Performance: 345.994 0.069 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.4%. 75: The balanceable part of the MD step is 68%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.9%. 75: 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 191.4 75: (ns/day) (hour/ns) 75: Performance: 469.719 0.051 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.7%. 75: The balanceable part of the MD step is 65%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.4%. 75: 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 191.1 75: (ns/day) (hour/ns) 75: Performance: 456.138 0.053 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.7%. 75: The balanceable part of the MD step is 62%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.1%. 75: 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 191.8 75: (ns/day) (hour/ns) 75: Performance: 459.095 0.052 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.9%. 75: The balanceable part of the MD step is 63%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.8%. 75: 75: 75: NOTE: 5 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.005 193.5 75: (ns/day) (hour/ns) 75: Performance: 318.838 0.075 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.8%. 75: The balanceable part of the MD step is 63%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.5%. 75: 75: 75: NOTE: 6 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.004 190.9 75: (ns/day) (hour/ns) 75: Performance: 393.008 0.061 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (235 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.047 0.024 198.1 75: (ns/day) (hour/ns) 75: Performance: 62.309 0.385 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 188.2 75: (ns/day) (hour/ns) 75: Performance: 453.352 0.053 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 189.0 75: (ns/day) (hour/ns) 75: Performance: 521.775 0.046 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 188.1 75: (ns/day) (hour/ns) 75: Performance: 453.151 0.053 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 5 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 188.7 75: (ns/day) (hour/ns) 75: Performance: 455.076 0.053 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 5 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 188.6 75: (ns/day) (hour/ns) 75: Performance: 481.146 0.050 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (375 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.015 0.008 195.0 75: (ns/day) (hour/ns) 75: Performance: 185.381 0.129 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.1 75: (ns/day) (hour/ns) 75: Performance: 457.901 0.052 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.7 75: (ns/day) (hour/ns) 75: Performance: 499.521 0.048 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.030 0.015 196.8 75: (ns/day) (hour/ns) 75: Performance: 96.222 0.249 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.8 75: (ns/day) (hour/ns) 75: Performance: 487.138 0.049 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 612.568 0.039 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (359 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 191.5 75: (ns/day) (hour/ns) 75: Performance: 476.660 0.050 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 190.0 75: (ns/day) (hour/ns) 75: Performance: 495.065 0.048 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.047 0.024 198.1 75: (ns/day) (hour/ns) 75: Performance: 62.136 0.386 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.8 75: (ns/day) (hour/ns) 75: Performance: 470.993 0.051 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.015 41.7 75: (ns/day) (hour/ns) 75: Performance: 95.385 0.252 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.011 52.5 75: (ns/day) (hour/ns) 75: Performance: 130.908 0.183 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (371 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.025 0.013 197.2 75: (ns/day) (hour/ns) 75: Performance: 117.390 0.204 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.023 0.012 196.1 75: (ns/day) (hour/ns) 75: Performance: 124.893 0.192 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 81 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.036 0.018 197.5 75: (ns/day) (hour/ns) 75: Performance: 81.283 0.295 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.032 0.016 197.3 75: (ns/day) (hour/ns) 75: Performance: 91.388 0.263 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 12 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.071 0.036 198.6 75: (ns/day) (hour/ns) 75: Performance: 41.252 0.582 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.015 0.015 97.1 75: (ns/day) (hour/ns) 75: Performance: 96.247 0.249 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (411 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 64 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.051 0.025 198.3 75: (ns/day) (hour/ns) 75: Performance: 57.660 0.416 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.031 0.016 197.2 75: (ns/day) (hour/ns) 75: Performance: 92.887 0.258 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.047 0.024 198.1 75: (ns/day) (hour/ns) 75: Performance: 61.627 0.389 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.047 0.024 198.1 75: (ns/day) (hour/ns) 75: Performance: 61.488 0.390 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 6 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.005 192.0 75: (ns/day) (hour/ns) 75: Performance: 321.921 0.075 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 5 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.004 191.5 75: (ns/day) (hour/ns) 75: Performance: 329.030 0.073 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (424 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.019 34.2 75: (ns/day) (hour/ns) 75: Performance: 75.867 0.316 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 191.2 75: (ns/day) (hour/ns) 75: Performance: 500.597 0.048 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 191.4 75: (ns/day) (hour/ns) 75: Performance: 549.317 0.044 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 192.2 75: (ns/day) (hour/ns) 75: Performance: 508.216 0.047 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 77 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.047 0.024 198.0 75: (ns/day) (hour/ns) 75: Performance: 61.448 0.391 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 85 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.047 0.024 198.1 75: (ns/day) (hour/ns) 75: Performance: 61.525 0.390 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (383 ms) 75: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (9304 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 22 tests from 1 test suite ran. (9470 ms total) 75: [ PASSED ] 22 tests. 75/81 Test #75: MdrunMpiCoordinationCouplingTestsTwoRanks ...... Passed 9.55 sec test 76 Start 76: MdrunMpiCoordinationConstraintsTestsOneRank 76: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-mpi-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMpiCoordinationConstraintsTestsOneRank.xml" 76: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 76: Test timeout computed to be: 1920 76: [==========] Running 10 tests from 1 test suite. 76: [----------] Global test environment set-up. 76: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.003 96.8 76: (ns/day) (hour/ns) 76: Performance: 584.164 0.041 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.014 0.015 99.4 76: (ns/day) (hour/ns) 76: Performance: 101.192 0.237 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.010 0.010 99.1 76: (ns/day) (hour/ns) 76: Performance: 145.713 0.165 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 97.6 76: (ns/day) (hour/ns) 76: Performance: 370.740 0.065 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 96.7 76: (ns/day) (hour/ns) 76: Performance: 564.364 0.043 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.4 76: (ns/day) (hour/ns) 76: Performance: 823.719 0.029 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (4147 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 97.6 76: (ns/day) (hour/ns) 76: Performance: 371.254 0.065 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.004 97.3 76: (ns/day) (hour/ns) 76: Performance: 409.097 0.059 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.001 0.002 94.8 76: (ns/day) (hour/ns) 76: Performance: 930.463 0.026 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 96.9 76: (ns/day) (hour/ns) 76: Performance: 437.449 0.055 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 97.2 76: (ns/day) (hour/ns) 76: Performance: 407.716 0.059 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 97.4 76: (ns/day) (hour/ns) 76: Performance: 457.526 0.052 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2483 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.8 76: (ns/day) (hour/ns) 76: Performance: 600.389 0.040 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.011 0.011 99.2 76: (ns/day) (hour/ns) 76: Performance: 136.152 0.176 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.4 76: (ns/day) (hour/ns) 76: Performance: 928.499 0.026 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.006 0.006 98.2 76: (ns/day) (hour/ns) 76: Performance: 254.833 0.094 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.2 76: (ns/day) (hour/ns) 76: Performance: 824.380 0.029 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.2 76: (ns/day) (hour/ns) 76: Performance: 706.490 0.034 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3545 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.003 96.5 76: (ns/day) (hour/ns) 76: Performance: 575.488 0.042 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.005 0.005 97.5 76: (ns/day) (hour/ns) 76: Performance: 311.739 0.077 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.2 76: (ns/day) (hour/ns) 76: Performance: 817.923 0.029 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 90.4 76: (ns/day) (hour/ns) 76: Performance: 802.579 0.030 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.8 76: (ns/day) (hour/ns) 76: Performance: 726.228 0.033 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.4 76: (ns/day) (hour/ns) 76: Performance: 771.521 0.031 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3716 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.007 29.0 76: (ns/day) (hour/ns) 76: Performance: 200.468 0.120 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.9 76: (ns/day) (hour/ns) 76: Performance: 899.882 0.027 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.001 0.002 94.3 76: (ns/day) (hour/ns) 76: Performance: 948.221 0.025 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.7 76: (ns/day) (hour/ns) 76: Performance: 769.017 0.031 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.010 0.010 98.9 76: (ns/day) (hour/ns) 76: Performance: 142.382 0.169 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 94.5 76: (ns/day) (hour/ns) 76: Performance: 796.148 0.030 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (4431 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 97.8 76: (ns/day) (hour/ns) 76: Performance: 468.415 0.051 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.003 97.8 76: (ns/day) (hour/ns) 76: Performance: 578.568 0.041 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.9 76: (ns/day) (hour/ns) 76: Performance: 616.491 0.039 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.003 97.3 76: (ns/day) (hour/ns) 76: Performance: 580.148 0.041 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.8 76: (ns/day) (hour/ns) 76: Performance: 719.948 0.033 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 97.9 76: (ns/day) (hour/ns) 76: Performance: 422.856 0.057 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3243 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.3 76: (ns/day) (hour/ns) 76: Performance: 347.095 0.069 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.010 19.4 76: (ns/day) (hour/ns) 76: Performance: 144.486 0.166 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.014 0.014 99.4 76: (ns/day) (hour/ns) 76: Performance: 104.834 0.229 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.2 76: (ns/day) (hour/ns) 76: Performance: 743.315 0.032 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.004 97.9 76: (ns/day) (hour/ns) 76: Performance: 415.723 0.058 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.8 76: (ns/day) (hour/ns) 76: Performance: 665.578 0.036 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (3982 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.7 76: (ns/day) (hour/ns) 76: Performance: 369.097 0.065 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 98.4 76: (ns/day) (hour/ns) 76: Performance: 562.098 0.043 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 98.2 76: (ns/day) (hour/ns) 76: Performance: 678.330 0.035 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 98.3 76: (ns/day) (hour/ns) 76: Performance: 826.814 0.029 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.006 0.006 99.2 76: (ns/day) (hour/ns) 76: Performance: 244.546 0.098 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 98.4 76: (ns/day) (hour/ns) 76: Performance: 576.133 0.042 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2451 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.010 0.010 99.5 76: (ns/day) (hour/ns) 76: Performance: 140.682 0.171 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 98.2 76: (ns/day) (hour/ns) 76: Performance: 787.800 0.030 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 98.8 76: (ns/day) (hour/ns) 76: Performance: 483.601 0.050 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.010 17.9 76: (ns/day) (hour/ns) 76: Performance: 148.951 0.161 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.011 0.011 99.4 76: (ns/day) (hour/ns) 76: Performance: 135.044 0.178 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 98.1 76: (ns/day) (hour/ns) 76: Performance: 624.174 0.038 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (3441 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.011 0.011 99.0 76: (ns/day) (hour/ns) 76: Performance: 130.901 0.183 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.007 0.007 98.5 76: (ns/day) (hour/ns) 76: Performance: 212.346 0.113 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.011 0.011 99.5 76: (ns/day) (hour/ns) 76: Performance: 137.455 0.175 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.7 76: (ns/day) (hour/ns) 76: Performance: 342.103 0.070 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.7 76: (ns/day) (hour/ns) 76: Performance: 343.591 0.070 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 98.0 76: (ns/day) (hour/ns) 76: Performance: 592.650 0.040 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (3748 ms) 76: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (35192 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 10 tests from 1 test suite ran. (35370 ms total) 76: [ PASSED ] 10 tests. 76/81 Test #76: MdrunMpiCoordinationConstraintsTestsOneRank .... Passed 35.42 sec test 77 Start 77: MdrunMpiCoordinationConstraintsTestsTwoRanks 77: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-mpi-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunMpiCoordinationConstraintsTestsTwoRanks.xml" 77: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 77: Test timeout computed to be: 1920 77: [==========] Running 10 tests from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 0.9%. 77: The balanceable part of the MD step is 62%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.6%. 77: 77: 77: NOTE: 72 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.046 0.023 198.6 77: (ns/day) (hour/ns) 77: Performance: 64.041 0.375 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.4%. 77: The balanceable part of the MD step is 59%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.4%. 77: 77: 77: NOTE: 68 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.037 0.019 198.2 77: (ns/day) (hour/ns) 77: Performance: 79.292 0.303 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 0.6%. 77: The balanceable part of the MD step is 54%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.3%. 77: 77: 77: NOTE: 26 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 190.9 77: (ns/day) (hour/ns) 77: Performance: 704.189 0.034 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.8%. 77: The balanceable part of the MD step is 50%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.9%. 77: 77: 77: NOTE: 28 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 190.7 77: (ns/day) (hour/ns) 77: Performance: 689.606 0.035 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 3.1%. 77: The balanceable part of the MD step is 51%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.6%. 77: 77: 77: NOTE: 28 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 191.7 77: (ns/day) (hour/ns) 77: Performance: 648.313 0.037 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 3.4%. 77: The balanceable part of the MD step is 50%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.7%. 77: 77: 77: NOTE: 29 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 191.3 77: (ns/day) (hour/ns) 77: Performance: 605.970 0.040 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (5864 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.4%. 77: The balanceable part of the MD step is 63%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.5%. 77: 77: 77: NOTE: 81 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.030 0.015 197.6 77: (ns/day) (hour/ns) 77: Performance: 96.314 0.249 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.8%. 77: The balanceable part of the MD step is 58%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.6%. 77: 77: 77: NOTE: 26 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 191.6 77: (ns/day) (hour/ns) 77: Performance: 594.308 0.040 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.2%. 77: The balanceable part of the MD step is 59%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.7%. 77: 77: 77: NOTE: 28 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 191.4 77: (ns/day) (hour/ns) 77: Performance: 632.083 0.038 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 3.5%. 77: The balanceable part of the MD step is 57%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 2.0%. 77: 77: 77: NOTE: 29 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 191.9 77: (ns/day) (hour/ns) 77: Performance: 553.960 0.043 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.0%. 77: The balanceable part of the MD step is 55%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.5%. 77: 77: 77: NOTE: 31 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 189.9 77: (ns/day) (hour/ns) 77: Performance: 575.380 0.042 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB got disabled because it was unsuitable to use. 77: Average load imbalance: 7.4%. 77: The balanceable part of the MD step is 53%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 3.9%. 77: 77: 77: NOTE: 27 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 192.3 77: (ns/day) (hour/ns) 77: Performance: 686.226 0.035 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (5678 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 193.5 77: (ns/day) (hour/ns) 77: Performance: 590.321 0.041 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 192.4 77: (ns/day) (hour/ns) 77: Performance: 710.196 0.034 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 7 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 191.5 77: (ns/day) (hour/ns) 77: Performance: 782.745 0.031 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 191.9 77: (ns/day) (hour/ns) 77: Performance: 589.277 0.041 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 191.1 77: (ns/day) (hour/ns) 77: Performance: 664.358 0.036 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 190.4 77: (ns/day) (hour/ns) 77: Performance: 692.746 0.035 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (4553 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 192.9 77: (ns/day) (hour/ns) 77: Performance: 593.335 0.040 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 191.5 77: (ns/day) (hour/ns) 77: Performance: 576.376 0.042 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 34 % of the run time was spent in domain decomposition, 77: 0 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: NOTE: 24 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.388 0.194 199.9 77: (ns/day) (hour/ns) 77: Performance: 7.570 3.170 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 189.6 77: (ns/day) (hour/ns) 77: Performance: 656.990 0.037 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 35 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 1.644 0.843 195.0 77: (ns/day) (hour/ns) 77: Performance: 1.743 13.771 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 191.7 77: (ns/day) (hour/ns) 77: Performance: 768.681 0.031 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (7304 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.030 0.015 197.9 77: (ns/day) (hour/ns) 77: Performance: 97.203 0.247 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 191.3 77: (ns/day) (hour/ns) 77: Performance: 646.273 0.037 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 192.5 77: (ns/day) (hour/ns) 77: Performance: 753.543 0.032 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 189.4 77: (ns/day) (hour/ns) 77: Performance: 564.726 0.042 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 190.7 77: (ns/day) (hour/ns) 77: Performance: 562.868 0.043 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 189.6 77: (ns/day) (hour/ns) 77: Performance: 611.564 0.039 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (5267 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.014 0.007 195.8 77: (ns/day) (hour/ns) 77: Performance: 203.784 0.118 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 192.9 77: (ns/day) (hour/ns) 77: Performance: 593.878 0.040 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.010 0.005 196.1 77: (ns/day) (hour/ns) 77: Performance: 274.445 0.087 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 11 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 2.548 1.300 196.0 77: (ns/day) (hour/ns) 77: Performance: 1.130 21.238 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.006 0.003 193.7 77: (ns/day) (hour/ns) 77: Performance: 517.132 0.046 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 192.1 77: (ns/day) (hour/ns) 77: Performance: 719.569 0.033 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (6188 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.038 0.019 198.5 77: (ns/day) (hour/ns) 77: Performance: 76.991 0.312 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 30 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 2.856 1.456 196.2 77: (ns/day) (hour/ns) 77: Performance: 1.009 23.790 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 191.1 77: (ns/day) (hour/ns) 77: Performance: 642.800 0.037 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 191.5 77: (ns/day) (hour/ns) 77: Performance: 577.565 0.042 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 190.5 77: (ns/day) (hour/ns) 77: Performance: 593.021 0.040 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.030 0.015 198.3 77: (ns/day) (hour/ns) 77: Performance: 97.431 0.246 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (7027 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.4%. 77: The balanceable part of the MD step is 69%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.0%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.006 0.003 193.6 77: (ns/day) (hour/ns) 77: Performance: 462.646 0.052 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 3.0%. 77: The balanceable part of the MD step is 7%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.2%. 77: 77: 77: NOTE: 54 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.027 0.014 198.0 77: (ns/day) (hour/ns) 77: Performance: 107.685 0.223 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB got disabled because it was unsuitable to use. 77: Average load imbalance: 3.2%. 77: The balanceable part of the MD step is 65%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 2.1%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 192.5 77: (ns/day) (hour/ns) 77: Performance: 551.975 0.043 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB got disabled because it was unsuitable to use. 77: Average load imbalance: 4.1%. 77: The balanceable part of the MD step is 57%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 2.4%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.024 0.012 197.4 77: (ns/day) (hour/ns) 77: Performance: 119.890 0.200 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.1%. 77: The balanceable part of the MD step is 65%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.3%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 189.4 77: (ns/day) (hour/ns) 77: Performance: 573.933 0.042 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.0%. 77: The balanceable part of the MD step is 61%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.2%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.009 0.007 125.7 77: (ns/day) (hour/ns) 77: Performance: 201.735 0.119 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (5856 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.015 0.008 195.1 77: (ns/day) (hour/ns) 77: Performance: 186.213 0.129 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.023 0.012 196.0 77: (ns/day) (hour/ns) 77: Performance: 124.425 0.193 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.009 0.007 130.7 77: (ns/day) (hour/ns) 77: Performance: 202.315 0.119 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.023 0.012 196.1 77: (ns/day) (hour/ns) 77: Performance: 125.013 0.192 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 70 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.039 0.020 197.7 77: (ns/day) (hour/ns) 77: Performance: 74.115 0.324 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 37 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 2.968 1.500 197.9 77: (ns/day) (hour/ns) 77: Performance: 0.979 24.506 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (7136 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.011 0.006 193.8 77: (ns/day) (hour/ns) 77: Performance: 261.713 0.092 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.015 0.008 193.9 77: (ns/day) (hour/ns) 77: Performance: 192.056 0.125 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.037 0.036 102.3 77: (ns/day) (hour/ns) 77: Performance: 40.484 0.593 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.039 0.020 197.7 77: (ns/day) (hour/ns) 77: Performance: 73.815 0.325 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.015 0.008 194.1 77: (ns/day) (hour/ns) 77: Performance: 194.004 0.124 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.032 0.016 197.2 77: (ns/day) (hour/ns) 77: Performance: 91.935 0.261 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (4895 ms) 77: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (59772 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 10 tests from 1 test suite ran. (59934 ms total) 77: [ PASSED ] 10 tests. 77/81 Test #77: MdrunMpiCoordinationConstraintsTestsTwoRanks ... Passed 59.98 sec test 78 Start 78: MdrunFEPTests 78: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunFEPTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 10 tests from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 10 tests from EquivalentToReference/FreeEnergyReferenceTest 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -221003823 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.669 0.335 199.9 78: (ns/day) (hour/ns) 78: Performance: 5.422 4.427 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (1016 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -8388675 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.535 0.268 199.9 78: (ns/day) (hour/ns) 78: Performance: 6.774 3.543 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (436 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: With PME there is a minor soft core effect present at the cut-off, 78: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 78: energy conservation, but usually other effects dominate. With a common 78: sigma value of 0.34 nm the fraction of the particle-particle potential at 78: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 4 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -8514 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.111 0.055 199.5 78: (ns/day) (hour/ns) 78: Performance: 32.695 0.734 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (137 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 78: and vdw_modifier=Force-switch 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 4 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 100 steps, 0.1 ps. 78: Setting the LD random seed to 2146418659 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.332 0.666 200.0 78: (ns/day) (hour/ns) 78: Performance: 13.104 1.831 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (824 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: WARNING 2 [file topol.top, line 72]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 3 [file topol.top, line 73]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 4 [file topol.top, line 98]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 5 [file topol.top, line 99]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 6 [file topol.top, line 100]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 7 [file topol.top, line 101]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 8 [file topol.top, line 111]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 9 [file topol.top, line 112]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 10 [file topol.top, line 113]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 11 [file topol.top, line 114]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 2 notes 78: 78: There were 11 warnings 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to 2146827759 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 5.134 2.567 200.0 78: (ns/day) (hour/ns) 78: Performance: 0.707 33.958 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (2716 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: WARNING 2 [file topol.top, line 72]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 3 [file topol.top, line 73]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 4 [file topol.top, line 98]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 5 [file topol.top, line 99]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 6 [file topol.top, line 100]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 7 [file topol.top, line 101]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 8 [file topol.top, line 111]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 9 [file topol.top, line 112]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 10 [file topol.top, line 113]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 11 [file topol.top, line 114]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: Removing center of mass motion in the presence of position restraints 78: might cause artifacts. When you are using position restraints to 78: equilibrate a macro-molecule, the artifacts are usually negligible. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There were 11 warnings 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -16777963 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.663 0.332 199.9 78: (ns/day) (hour/ns) 78: Performance: 5.471 4.387 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (407 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 2 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -69599502 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.331 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.88 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.100 0.050 199.5 78: (ns/day) (hour/ns) 78: Performance: 36.041 0.666 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (145 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There was 1 note 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.276 0.138 199.8 78: (ns/day) (hour/ns) 78: Performance: 13.129 1.828 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to 2145368829 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between excluded atoms is 0.331 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.88 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (258 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: With PME there is a minor soft core effect present at the cut-off, 78: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 78: energy conservation, but usually other effects dominate. With a common 78: sigma value of 0.34 nm the fraction of the particle-particle potential at 78: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -97060882 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.270 0.135 199.8 78: (ns/day) (hour/ns) 78: Performance: 13.410 1.790 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (267 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: With PME there is a minor soft core effect present at the cut-off, 78: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 78: energy conservation, but usually other effects dominate. With a common 78: sigma value of 0.34 nm the fraction of the particle-particle potential at 78: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -270565515 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.172 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.88 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: NOTE: 0 % of the run time was spent in domain decomposition, 78: 10 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.128 0.064 199.6 78: (ns/day) (hour/ns) 78: Performance: 28.334 0.847 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (152 ms) 78: [----------] 10 tests from EquivalentToReference/FreeEnergyReferenceTest (6365 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 10 tests from 1 test suite ran. (6553 ms total) 78: [ PASSED ] 10 tests. 78/81 Test #78: MdrunFEPTests .................................. Passed 6.61 sec test 79 Start 79: MdrunPullTests 79: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunPullTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 4 tests from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 4 tests from PullTest/PullIntegrationTest 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1293.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.122 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.575 nm 0.600 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 11 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.279 0.139 199.8 79: (ns/day) (hour/ns) 79: Performance: 13.010 1.845 79: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (1036 ms) 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1293.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.122 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.301 nm 0.400 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.167 0.084 199.7 79: (ns/day) (hour/ns) 79: Performance: 21.719 1.105 79: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (1132 ms) 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Pull group 3 'r_3' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1292.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.357 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.575 nm 0.500 nm 79: 1 3 2 79: 3 3 8 0.331 nm 0.400 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.132 0.066 199.7 79: (ns/day) (hour/ns) 79: Performance: 27.424 0.875 79: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (917 ms) 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1293.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.122 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.575 nm 0.000 nm 79: 1 3 2 79: 2 3 5 0.050 nm 0.000 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.124 0.062 199.5 79: (ns/day) (hour/ns) 79: Performance: 29.159 0.823 79: Opened /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (600 ms) 79: [----------] 4 tests from PullTest/PullIntegrationTest (3686 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 4 tests from 1 test suite ran. (3852 ms total) 79: [ PASSED ] 4 tests. 79/81 Test #79: MdrunPullTests ................................. Passed 3.91 sec test 80 Start 80: MdrunSimulatorComparison 80: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml" 80: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 0 tests from 0 test suites. 80: [==========] 0 tests from 0 test suites ran. (0 ms total) 80: [ PASSED ] 0 tests. 80: 80: YOU HAVE 82 DISABLED TESTS 80: 80/81 Test #80: MdrunSimulatorComparison ....................... Passed 0.03 sec test 81 Start 81: MdrunVirtualSiteTests 81: Test command: /build/reproducible-path/gromacs-2022.5/build/basic/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic/Testing/Temporary/MdrunVirtualSiteTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 37 tests from 2 test suites. 81: [----------] Global test environment set-up. 81: [----------] 1 test from VirtualSiteVelocityTest 81: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 81: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 81: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 81: 81: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.0%. 81: The balanceable part of the MD step is 51%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.0%. 81: 81: 81: NOTE: 53 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.029 0.015 198.3 81: (ns/day) (hour/ns) 81: Performance: 53.013 0.453 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: trr version: GMX_trn_file (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (72 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.9%. 81: The balanceable part of the MD step is 47%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.4%. 81: 81: 81: NOTE: 29 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 190.0 81: (ns/day) (hour/ns) 81: Performance: 345.442 0.069 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (55 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 17 % of the run time was spent in domain decomposition, 81: 2 % of the run time was spent in pair search, 81: you might want to increase nstlist (this has no effect on accuracy) 81: 81: NOTE: 24 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.024 18.7 81: (ns/day) (hour/ns) 81: Performance: 32.899 0.729 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (75 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 29 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 187.8 81: (ns/day) (hour/ns) 81: Performance: 348.897 0.069 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (83 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 179.3 81: (ns/day) (hour/ns) 81: Performance: 348.729 0.069 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (67 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 5 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 189.9 81: (ns/day) (hour/ns) 81: Performance: 382.109 0.063 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (72 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 5 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 189.6 81: (ns/day) (hour/ns) 81: Performance: 363.397 0.066 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (83 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 5 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 27 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 188.8 81: (ns/day) (hour/ns) 81: Performance: 360.605 0.067 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (111 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.3%. 81: The balanceable part of the MD step is 51%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.1%. 81: 81: 81: NOTE: 27 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 191.4 81: (ns/day) (hour/ns) 81: Performance: 351.530 0.068 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (47 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 88 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.014 197.8 81: (ns/day) (hour/ns) 81: Performance: 55.243 0.434 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (83 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 15 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.009 0.021 42.4 81: (ns/day) (hour/ns) 81: Performance: 37.858 0.634 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (107 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 68 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.037 0.019 198.0 81: (ns/day) (hour/ns) 81: Performance: 41.958 0.572 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (99 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 27 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 191.4 81: (ns/day) (hour/ns) 81: Performance: 414.289 0.058 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (79 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.014 30.7 81: (ns/day) (hour/ns) 81: Performance: 54.571 0.440 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (107 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 14 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.007 62.9 81: (ns/day) (hour/ns) 81: Performance: 119.622 0.201 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (72 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 31 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 190.8 81: (ns/day) (hour/ns) 81: Performance: 422.993 0.057 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (107 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 30 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 190.2 81: (ns/day) (hour/ns) 81: Performance: 354.125 0.068 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (75 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 30 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.003 0.002 190.6 81: (ns/day) (hour/ns) 81: Performance: 434.373 0.055 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (64 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 29 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 190.7 81: (ns/day) (hour/ns) 81: Performance: 344.184 0.070 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (83 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 81: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (1557 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 37 tests from 2 test suites ran. (1707 ms total) 81: [ PASSED ] 37 tests. 81/81 Test #81: MdrunVirtualSiteTests .......................... Passed 1.73 sec 100% tests passed, 0 tests failed out of 81 Label Time Summary: GTest = 235.08 sec*proc (79 tests) IntegrationTest = 74.74 sec*proc (23 tests) MpiTest = 144.34 sec*proc (19 tests) QuickGpuTest = 22.59 sec*proc (15 tests) SlowTest = 146.03 sec*proc (13 tests) UnitTest = 14.30 sec*proc (43 tests) Total Test time (real) = 235.86 sec /usr/bin/make -j15 -C build/basic-dp tests make[1]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2022.5 -B/build/reproducible-path/gromacs-2022.5/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2022.5 -B/build/reproducible-path/gromacs-2022.5/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start 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CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/test_device.cpp.o CMakeFiles/testutils.dir/test_hardware_environment.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/trajectoryreader.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend /usr/bin/make -f 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Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -MF CMakeFiles/testutils-test.dir/refdata_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/tests/refdata_tests.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/tests/mpitest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/simulatorcomparison.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -MF CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build /usr/bin/make -f src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build.make src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/alignedallocator.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests/awh_setup.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/calc_verletbuf.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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/usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.7.0.0 ../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast 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CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/arrayref.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests/biassharing.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target applied_forces-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target nblib_test_infrastructure /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/tests/hashedmap.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target testutils-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -MF CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o.d -o CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests/bias_fep_lambda_state.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/tests/position_restraints.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fft/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target nbnxm-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/hardware/tests 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src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/device_availability.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/leapfrog.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/leapfrogtestdata.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 64%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/settle.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 65%] Built target domdec-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -MF CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o.d -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/tests/accessor_policy.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 65%] Built target listed_forces-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 66%] Built target awh-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include 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src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/tests/mockhardwaretopology.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests/helpmanager.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 66%] Built target fft-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/abstractoptionstorage.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 66%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF 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/build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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'/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/mdspan.cpp.o -MF CMakeFiles/mdspan-test.dir/mdspan.cpp.o.d -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/tests/mdspan.cpp /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/manager.cpp.o -MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/tests/checkpointdata.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 68%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tables/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/tests/mshift.cpp /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/tests/pbc.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 69%] Built target mdlib-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/timing/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/timing/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/tests/device_management.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 69%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include 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-I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 69%] Built target timing-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/tabulatednormaldistribution.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 70%] Built target hardware-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 70%] Built target mdspan-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/compat/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/compat/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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70%] Built target pbcutil-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 72%] Built target taskassignment-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/optionsassigner.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lmuparser -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 72%] Built target pull-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/genconf.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 73%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 74%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/tests/gmx_mindist.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem 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CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/tests/gmx_traj.cpp [ 74%] Built target table-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/tests/autocorr.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" 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-I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 76%] Built target gmxana-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/datatest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 76%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/builder.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 76%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/legacyenergy.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 77%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/treesupport.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/cstringutil.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 77%] Built target ewald-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/mock_datamodule.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 77%] Built target mdtypes-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/random/tests/CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem 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'/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 78%] Built target correlations-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make 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CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests/report_methods.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 78%] Built target energyanalysis-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 80%] Built target random-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -MF CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o.d -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/outputadapters.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 81%] Built target topology-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/multiple_time_stepping.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests/trjconv.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 82%] Built target options-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/exactcontinuation.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 82%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/trajectory_writing.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/freezegroups.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 [ 82%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/domain_decomposition.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 82%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/multisim.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 82%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_integer.cpp.o -MF CMakeFiles/simd-test.dir/simd_integer.cpp.o.d -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_integer.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/nonbonded_bench.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 82%] Built target mdrun-tpi-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/vectypes.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 82%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/initialconstraints.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd 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/build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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/build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 82%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF 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../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 82%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/logger.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 84%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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-I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/message_string_collector.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 85%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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'/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 85%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make 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CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/path.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/selectionoption.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 85%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 85%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/simulator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 86%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem 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-DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 88%] Built target simd-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include 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src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-mpi-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 88%] Built target mdrun-mpi-coordination-basic-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/box.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 88%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include 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-I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 88%] Built target mdrun-fep-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/gmxcalculator.cpp /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/bondtypes.cpp In file included from /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include/gtest/gtest.h:60, from /build/reproducible-path/gromacs-2022.5/api/nblib/tests/tpr.cpp:43: /build/reproducible-path/gromacs-2022.5/api/nblib/tests/tpr.cpp: In member function 'virtual void nblib::test::TprReaderTest_Spc2Reads_Test::TestBody()': /build/reproducible-path/gromacs-2022.5/api/nblib/tests/tpr.cpp:91:48: warning: ignoring return value of 'std::vector<_Tp, _Alloc>::size_type std::vector<_Tp, _Alloc>::size() const [with _Tp = gmx::BasicVector; _Alloc = std::allocator >; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 91 | EXPECT_NO_THROW(tprReader.coordinates_.size()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/12/vector:64, from /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include/gtest/gtest.h:58: /usr/include/c++/12/bits/stl_vector.h:987:7: note: declared here 987 | size() const _GLIBCXX_NOEXCEPT | ^~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 88%] Built target mdrun-mpi-coordination-constraints-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/util/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/util/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/util/tests/setup.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 89%] Built target mdrun-mpi-coordination-coupling-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 89%] Built target mdrun-simulator-comparison-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 89%] Built target mdrun-non-integrator-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/template_mp.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 ../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 89%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 90%] Built target mdrun-vsites-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 ../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/particletype.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 90%] Built target nblib-util-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/moduletest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 90%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 90%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 92%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlineparser.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 93%] Built target selection-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/angle.cpp [ 93%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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-I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF 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/build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem 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CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 94%] Built target math-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -MF CMakeFiles/analysisdata-test.dir/lifetime.cpp.o.d -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include 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-funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include 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-funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 ../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/calculator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 96%] Built target utility-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/conversions.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 96%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/msd.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 96%] Built target commandline-test cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem 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../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 96%] Built target analysisdata-test In member function 'virtual void {anonymous}::UnionFinderTest_WorksEmpty_Test::TestBody()': cc1plus: warning: iteration 2147483648 invokes undefined behavior [-Waggressive-loop-optimizations] In file included from /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/unionfind.cpp:43: In member function 'std::vector gmx::UnionFinder::allSizes()', inlined from 'virtual void {anonymous}::UnionFinderTest_WorksEmpty_Test::TestBody()' at /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/unionfind.cpp:60:5: /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/unionfind.h:118:27: note: within this loop 118 | for (int i = 0; i < count; ++i) | ~~^~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 ../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 97%] Built target trajectoryanalysis-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 98%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [ 98%] Built target nblib-tests cd /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 ../../../../lib/libgromacs_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [100%] Built target nblib-listed-forces-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' cd /build/reproducible-path/gromacs-2022.5/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp /build/reproducible-path/gromacs-2022.5/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2022.5/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' make[1]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2022.5/build/basic-dp/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2022.5/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2022.5/build/basic-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2022.5/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2022.5/build/basic-dp/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2022.5/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: NbLibListedForcesTests 1: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/listed_forces/tests 1: Test timeout computed to be: 600 1: [==========] Running 44 tests from 22 test suites. 1: [----------] Global test environment set-up. 1: [----------] 8 tests from NBlibTest 1: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 1: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 1: [ RUN ] NBlibTest.BondTypesLessThanWorks 1: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 1: [ RUN ] NBlibTest.CanSplitListedWork 1: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 1: [ RUN ] NBlibTest.ListedForceBuffer 1: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 1: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 1: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (12 ms) 1: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 1: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 1: [ RUN ] NBlibTest.EndToEndListedComparison 1: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 1: [ RUN ] NBlibTest.shiftForcesAreCorrect 1: [ OK ] NBlibTest.shiftForcesAreCorrect (79 ms) 1: [----------] 8 tests from NBlibTest (92 ms total) 1: 1: [----------] 1 test from Kernels 1: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 1: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 1: [----------] 1 test from Kernels (0 ms total) 1: 1: [----------] 1 test from FourCenter 1: [ RUN ] FourCenter.ListedForcesProperDihedralTest 1: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 1: [----------] 1 test from FourCenter (0 ms total) 1: 1: [----------] 7 tests from ThreeCenter 1: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 1: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 1: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 1: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 1: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 1: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 1: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 1: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 1: [----------] 7 tests from ThreeCenter (0 ms total) 1: 1: [----------] 5 tests from TwoCenter 1: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 1: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 1: [ RUN ] TwoCenter.ListedForcesG96BondTest 1: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 1: [ RUN ] TwoCenter.ListedForcesCubicBondTest 1: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 1: [ RUN ] TwoCenter.ListedForcesMorseBondTest 1: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 1: [ RUN ] TwoCenter.ListedForcesFeneBondTest 1: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 1: [----------] 5 tests from TwoCenter (0 ms total) 1: 1: [----------] 5 tests from ListedExampleData 1: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 1: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 1: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 1: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 1: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 1: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 1: [ RUN ] ListedExampleData.CanReduceForces 1: [ OK ] ListedExampleData.CanReduceForces (0 ms) 1: [ RUN ] ListedExampleData.CanReduceEnergies 1: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 1: [----------] 5 tests from ListedExampleData (0 ms total) 1: 1: [----------] 1 test from LinearChainDataFixture 1: [ RUN ] LinearChainDataFixture.Multithreading 1: [ OK ] LinearChainDataFixture.Multithreading (50 ms) 1: [----------] 1 test from LinearChainDataFixture (50 ms total) 1: 1: [----------] 2 tests from ListedShims 1: [ RUN ] ListedShims.ParameterConversion 1: [ OK ] ListedShims.ParameterConversion (0 ms) 1: [ RUN ] ListedShims.GmxToNblibConversion 1: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 1: [----------] 2 tests from ListedShims (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 1: 1: [----------] 1 test from ListedTransformations 1: [ RUN ] ListedTransformations.SortInteractionIndices 1: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 1: [----------] 1 test from ListedTransformations (0 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 44 tests from 22 test suites ran. (147 ms total) 1: [ PASSED ] 44 tests. 1/81 Test #1: NbLibListedForcesTests ......................... Passed 0.25 sec test 2 Start 2: NbLibSamplesTestArgon 2: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/argon-forces-integration 2: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/samples 2: Test timeout computed to be: 1500 2: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 2: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189 2: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 2: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 2/81 Test #2: NbLibSamplesTestArgon .......................... Passed 0.03 sec test 3 Start 3: NbLibSamplesTestMethaneWater 3: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/methane-water-integration 3: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/samples 3: Test timeout computed to be: 1500 3: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 3: final position of particle 9: x 77.358372 y 5.325207 z -80.600064 3/81 Test #3: NbLibSamplesTestMethaneWater ................... Passed 0.15 sec test 4 Start 4: NbLibUtilTests 4: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml" 4: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/util/tests 4: Test timeout computed to be: 30 4: [==========] Running 16 tests from 2 test suites. 4: [----------] Global test environment set-up. 4: [----------] 6 tests from NBlibTest 4: [ RUN ] NBlibTest.isRealValued 4: [ OK ] NBlibTest.isRealValued (0 ms) 4: [ RUN ] NBlibTest.checkNumericValuesHasNan 4: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 4: [ RUN ] NBlibTest.checkNumericValuesHasInf 4: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 4: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 4: Velocities were taken from a Maxwell distribution at 300 K 4: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 4: [ RUN ] NBlibTest.generateVelocitySize 4: Velocities were taken from a Maxwell distribution at 300 K 4: [ OK ] NBlibTest.generateVelocitySize (0 ms) 4: [ RUN ] NBlibTest.generateVelocityCheckNumbers 4: Velocities were taken from a Maxwell distribution at 300 K 4: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 4: [----------] 6 tests from NBlibTest (0 ms total) 4: 4: [----------] 10 tests from NblibTraitsUtils 4: [ RUN ] NblibTraitsUtils.FuseTwo 4: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 4: [ RUN ] NblibTraitsUtils.Fuse 4: [ OK ] NblibTraitsUtils.Fuse (0 ms) 4: [ RUN ] NblibTraitsUtils.Repeat 4: [ OK ] NblibTraitsUtils.Repeat (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTuple1 4: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTuple2 4: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 4: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 4: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 4: [ RUN ] NblibTraitsUtils.Contains 4: [ OK ] NblibTraitsUtils.Contains (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 4: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 4: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 4: [----------] 10 tests from NblibTraitsUtils (0 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 16 tests from 2 test suites ran. (0 ms total) 4: [ PASSED ] 16 tests. 4/81 Test #4: NbLibUtilTests ................................. Passed 0.06 sec test 5 Start 5: NbLibSetupTests 5: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml" 5: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests 5: Test timeout computed to be: 600 5: [==========] Running 56 tests from 3 test suites. 5: [----------] Global test environment set-up. 5: [----------] 41 tests from NBlibTest 5: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 5: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 5: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 5: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 5: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 5: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 5: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 5: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 5: [ RUN ] NBlibTest.CubicBoxWorks 5: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 5: [ RUN ] NBlibTest.BoxEqual 5: [ OK ] NBlibTest.BoxEqual (0 ms) 5: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 5: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 5: [ RUN ] NBlibTest.CanMergeInteractions 5: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 5: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 5: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 5: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 5: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 5: [ RUN ] NBlibTest.PbcHolderWorks 5: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 5: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 5: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 5: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 5: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 5: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 5: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 5: [ RUN ] NBlibTest.AtWorks 5: [ OK ] NBlibTest.AtWorks (0 ms) 5: [ RUN ] NBlibTest.AtThrows 5: [ OK ] NBlibTest.AtThrows (0 ms) 5: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 5: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 5: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 5: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 5: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 5: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 5: [ RUN ] NBlibTest.CanAddInteractions 5: [ OK ] NBlibTest.CanAddInteractions (0 ms) 5: [ RUN ] NBlibTest.CanAddUreyBradley 5: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 5: [ RUN ] NBlibTest.TopologyHasNumParticles 5: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 5: [ RUN ] NBlibTest.TopologyHasCharges 5: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 5: [ RUN ] NBlibTest.TopologyHasMasses 5: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 5: [ RUN ] NBlibTest.TopologyHasParticleTypes 5: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 5: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 5: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 5: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 5: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 5: [ RUN ] NBlibTest.TopologyHasExclusions 5: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 5: [ RUN ] NBlibTest.TopologyHasSequencing 5: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 5: [ RUN ] NBlibTest.TopologyCanAggregateBonds 5: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 5: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 5: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 5: [ RUN ] NBlibTest.TopologySequenceIdThrows 5: No particle O-Atom in residue SOL in molecule SOL found 5: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 5: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 5: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 5: [ RUN ] NBlibTest.TopologyListedInteractions 5: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 5: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 5: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 5: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 5: No particle Iron in residue SOL in molecule SOL found 5: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 5: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 5: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 5: [----------] 41 tests from NBlibTest (3 ms total) 5: 5: [----------] 14 tests from NbnxmSetupTest 5: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 5: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 5: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 5: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 5: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 5: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 5: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 5: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 5: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 5: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 5: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 5: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 5: [ RUN ] NbnxmSetupTest.updateForcerecWorks 5: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 5: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 5: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 5: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 5: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 5: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 5: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (8 ms) 5: [----------] 14 tests from NbnxmSetupTest (8 ms total) 5: 5: [----------] 1 test from VirialsTest 5: [ RUN ] VirialsTest.computeVirialTensorWorks 5: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 5: [----------] 1 test from VirialsTest (0 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 56 tests from 3 test suites ran. (12 ms total) 5: [ PASSED ] 56 tests. 5/81 Test #5: NbLibSetupTests ................................ Passed 0.22 sec test 6 Start 6: NbLibTprTests 6: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/NbLibTprTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests 6: Test timeout computed to be: 30 6: [==========] Running 4 tests from 1 test suite. 6: [----------] Global test environment set-up. 6: [----------] 4 tests from TprReaderTest 6: [ RUN ] TprReaderTest.SimDBTprIsCreated 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Number of degrees of freedom in T-Coupling group System is 33.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 6: NVE simulation: will use the initial temperature of 68.810 K for 6: determining the Verlet buffer size 6: 6: 6: There were 3 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 6: Generated 1 of the 1 non-bonded parameter combinations 6: 6: Excluding 1 bonded neighbours molecule type 'Argon' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.SimDBTprIsCreated (64 ms) 6: [ RUN ] TprReaderTest.Spc2Reads 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Generating 1-4 interactions: fudge = 0.5 6: Number of degrees of freedom in T-Coupling group System is 9.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: NVE simulation: will use the initial temperature of 2573.591 K for 6: determining the Verlet buffer size 6: 6: 6: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: You are using a plain Coulomb cut-off, which might produce artifacts. 6: You might want to consider using PME electrostatics. 6: 6: 6: 6: There were 4 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 6: Generated 3 of the 3 non-bonded parameter combinations 6: 6: Generated 3 of the 3 1-4 parameter combinations 6: 6: Excluding 2 bonded neighbours molecule type 'SOL' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.Spc2Reads (67 ms) 6: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Number of degrees of freedom in T-Coupling group System is 33.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 6: NVE simulation: will use the initial temperature of 68.810 K for 6: determining the Verlet buffer size 6: 6: 6: There were 3 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 6: Generated 1 of the 1 non-bonded parameter combinations 6: 6: Excluding 1 bonded neighbours molecule type 'Argon' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (68 ms) 6: [ RUN ] TprReaderTest.FCfromTprDataWorks 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Number of degrees of freedom in T-Coupling group System is 33.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 6: NVE simulation: will use the initial temperature of 68.810 K for 6: determining the Verlet buffer size 6: 6: 6: There were 3 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 6: Generated 1 of the 1 non-bonded parameter combinations 6: 6: Excluding 1 bonded neighbours molecule type 'Argon' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.FCfromTprDataWorks (51 ms) 6: [----------] 4 tests from TprReaderTest (252 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 4 tests from 1 test suite ran. (413 ms total) 6: [ PASSED ] 4 tests. 6/81 Test #6: NbLibTprTests .................................. Passed 0.47 sec test 7 Start 7: NbLibIntegrationTests 7: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 20 tests from 1 test suite. 7: [----------] Global test environment set-up. 7: [----------] 20 tests from NBlibTest 7: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 7: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 7: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 7: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 7: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 7: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 7: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 7: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (4 ms) 7: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 7: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 7: [ RUN ] NBlibTest.ExpectedNumberOfForces 7: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 7: [ RUN ] NBlibTest.CanIntegrateSystem 7: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 7: [ RUN ] NBlibTest.UpdateChangesForces 7: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 7: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 7: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 7: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 7: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 7: [ RUN ] NBlibTest.CanConstructSimulationState 7: [ OK ] NBlibTest.CanConstructSimulationState (4 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 7: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 7: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 7: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 7: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 7: [ RUN ] NBlibTest.SimulationStateCanMove 7: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 7: [ RUN ] NBlibTest.SimulationStateCanAssign 7: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 7: [ RUN ] NBlibTest.SimulationStateHasBox 7: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 7: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 7: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 7: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 7: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 7: [----------] 20 tests from NBlibTest (16 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 20 tests from 1 test suite ran. (16 ms total) 7: [ PASSED ] 20 tests. 7/81 Test #7: NbLibIntegrationTests .......................... Passed 0.08 sec test 8 Start 8: NbLibIntegratorTests 8: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/api/nblib/tests 8: Test timeout computed to be: 600 8: [==========] Running 1 test from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 1 test from NBlibTest 8: [ RUN ] NBlibTest.IntegratorWorks 8: [ OK ] NBlibTest.IntegratorWorks (0 ms) 8: [----------] 1 test from NBlibTest (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 1 test from 1 test suite ran. (0 ms total) 8: [ PASSED ] 1 test. 8/81 Test #8: NbLibIntegratorTests ........................... Passed 0.06 sec test 9 Start 9: TestUtilsUnitTests 9: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/testutils/tests 9: Test timeout computed to be: 30 9: [==========] Running 59 tests from 5 test suites. 9: [----------] Global test environment set-up. 9: [----------] 10 tests from InteractiveTestHelperTest 9: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 9: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 9: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 9: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 9: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 9: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 9: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 9: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 9: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 9: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 9: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 9: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 9: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 9: [----------] 10 tests from InteractiveTestHelperTest (3 ms total) 9: 9: [----------] 34 tests from ReferenceDataTest 9: [ RUN ] ReferenceDataTest.HandlesSimpleData 9: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 9: [ OK ] ReferenceDataTest.HandlesFloatingPointData (4 ms) 9: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 9: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesStringBlockData 9: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesVectorData 9: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSequenceData 9: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 9: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesIncorrectData 9: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 9: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMissingData 9: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUncheckedData 9: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 9: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 9: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesAnys 9: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 9: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 9: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 9: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 9: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 9: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 9: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 9: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 9: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 9: [ OK ] ReferenceDataTest.HandlesEmptyStrings (8 ms) 9: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 9: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 9: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 9: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 9: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 9: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesReadingValues 9: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 9: [----------] 34 tests from ReferenceDataTest (19 ms total) 9: 9: [----------] 7 tests from FloatingPointDifferenceTest 9: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 9: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 9: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 9: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 9: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 9: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 9: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 9: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 9: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 9: 9: [----------] 4 tests from FloatingPointToleranceTest 9: [ RUN ] FloatingPointToleranceTest.UlpTolerance 9: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 9: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 9: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 9: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 9: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 9: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 9: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 9: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 9: 9: [----------] 4 tests from XvgTests 9: [ RUN ] XvgTests.CreateFile 9: [ OK ] XvgTests.CreateFile (0 ms) 9: [ RUN ] XvgTests.CheckMissing 9: [ OK ] XvgTests.CheckMissing (0 ms) 9: [ RUN ] XvgTests.CheckExtra 9: [ OK ] XvgTests.CheckExtra (4 ms) 9: [ RUN ] XvgTests.ReadIncorrect 9: [ OK ] XvgTests.ReadIncorrect (0 ms) 9: [----------] 4 tests from XvgTests (6 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 59 tests from 5 test suites ran. (37 ms total) 9: [ PASSED ] 59 tests. 9/81 Test #9: TestUtilsUnitTests ............................. Passed 0.08 sec test 10 Start 10: TestUtilsMpiUnitTests 10: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/testutils/tests 10: Test timeout computed to be: 30 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from MpiSelfTest 10: [ RUN ] MpiSelfTest.Runs 10: [ OK ] MpiSelfTest.Runs (23 ms) 10: [----------] 1 test from MpiSelfTest (23 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (23 ms total) 10: [ PASSED ] 1 test. 10/81 Test #10: TestUtilsMpiUnitTests .......................... Passed 0.08 sec test 11 Start 11: UtilityUnitTests 11: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests 11: Test timeout computed to be: 30 11: [==========] Running 386 tests from 61 test suites. 11: [----------] Global test environment set-up. 11: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.Move 11: [ OK ] AllocatorTest/0.Move (0 ms) 11: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/0 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.Move 11: [ OK ] AllocatorTest/1.Move (0 ms) 11: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/1 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.Move 11: [ OK ] AllocatorTest/2.Move (0 ms) 11: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/2 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.Move 11: [ OK ] AllocatorTest/3.Move (0 ms) 11: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/3 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 11: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/4.Move 11: [ OK ] AllocatorTest/4.Move (0 ms) 11: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/4 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 11: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/5.Move 11: [ OK ] AllocatorTest/5.Move (0 ms) 11: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/5 (0 ms total) 11: 11: [----------] 1 test from AllocatorUntypedTest 11: [ RUN ] AllocatorUntypedTest.Comparison 11: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 11: [----------] 1 test from AllocatorUntypedTest (0 ms total) 11: 11: [----------] 4 tests from EmptyArrayRefTest 11: [ RUN ] EmptyArrayRefTest.IsEmpty 11: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 11: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 11: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 11: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 11: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 11: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 11: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 11: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 11: 11: [----------] 1 test from EmptyConstArrayRefTest 11: [ RUN ] EmptyConstArrayRefTest.IsEmpty 11: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 11: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/13 (4 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 11: 11: [----------] 2 tests from CStringUtilityTest 11: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 11: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 11: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 11: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 11: [----------] 2 tests from CStringUtilityTest (0 ms total) 11: 11: [----------] 2 tests from DefaultInitializationAllocator 11: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 11: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 11: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 11: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 11: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 11: 11: [----------] 4 tests from EnumerationHelpersTest 11: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 11: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 11: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 11: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 11: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 11: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 11: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 11: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 11: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 11: 11: [----------] 9 tests from FixedCapacityVectorTest 11: [ RUN ] FixedCapacityVectorTest.IsEmpty 11: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 11: [ RUN ] FixedCapacityVectorTest.PushWorks 11: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.PopWorks 11: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.ClearWorks 11: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 11: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.AtThrows 11: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 11: [ RUN ] FixedCapacityVectorTest.IteratorWorks 11: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 11: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 11: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 11: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 11: 11: [----------] 5 tests from InMemorySerializerTest 11: [ RUN ] InMemorySerializerTest.Roundtrip 11: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 11: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 11: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 11: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 11: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 11: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 11: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 11: [ RUN ] InMemorySerializerTest.SizeIsCorrect 11: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 11: [----------] 5 tests from InMemorySerializerTest (0 ms total) 11: 11: [----------] 4 tests from KeyValueTreeSerializerTest 11: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 11: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 11: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 11: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 11: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 11: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 11: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 11: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 11: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 11: 11: [----------] 6 tests from TreeValueTransformTest 11: [ RUN ] TreeValueTransformTest.SimpleTransforms 11: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 11: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 11: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 11: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 11: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 11: [ RUN ] TreeValueTransformTest.ObjectFromString 11: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 11: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 11: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 11: [ RUN ] TreeValueTransformTest.ScopedTransformRules 11: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 11: [----------] 6 tests from TreeValueTransformTest (1 ms total) 11: 11: [----------] 1 test from TreeValueTransformErrorTest 11: [ RUN ] TreeValueTransformErrorTest.ConversionError 11: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 11: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 11: 11: [----------] 9 tests from ListOfLists 11: [ RUN ] ListOfLists.EmptyListOfListsWorks 11: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 11: [ RUN ] ListOfLists.AppendWorks 11: [ OK ] ListOfLists.AppendWorks (0 ms) 11: [ RUN ] ListOfLists.EmptyListWorks 11: [ OK ] ListOfLists.EmptyListWorks (0 ms) 11: [ RUN ] ListOfLists.AppendAccessWorks 11: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 11: [ RUN ] ListOfLists.ClearWorks 11: [ OK ] ListOfLists.ClearWorks (0 ms) 11: [ RUN ] ListOfLists.OutOfRangeAccessThrows 11: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 11: [ RUN ] ListOfLists.FrontAndBackWork 11: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 11: [ RUN ] ListOfLists.ExtractsAndRestores 11: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 11: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 11: [ OK ] ListOfLists.AppendsListOfListsWithOffset (8 ms) 11: [----------] 9 tests from ListOfLists (8 ms total) 11: 11: [----------] 7 tests from LoggerTest 11: [ RUN ] LoggerTest.EmptyLoggerWorks 11: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 11: [ RUN ] LoggerTest.LogsToStream 11: [ OK ] LoggerTest.LogsToStream (0 ms) 11: [ RUN ] LoggerTest.LogsToFile 11: [ OK ] LoggerTest.LogsToFile (0 ms) 11: [ RUN ] LoggerTest.LevelFilteringWorks 11: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 11: [ RUN ] LoggerTest.LogsToMultipleStreams 11: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 11: [ RUN ] LoggerTest.LogsToMultipleFiles 11: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 11: [ RUN ] LoggerTest.LogsToStreamAndFile 11: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 11: [----------] 7 tests from LoggerTest (1 ms total) 11: 11: [----------] 4 tests from MDModulesNotifierTest 11: [ RUN ] MDModulesNotifierTest.AddConsumer 11: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 11: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 11: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 11: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 11: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 11: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 11: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 11: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 11: 11: [----------] 7 tests from MessageStringCollectorTest 11: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 11: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 11: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 11: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 11: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 11: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 11: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanMoveAssign 11: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 11: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 11: 11: [----------] 1 test from PathTest 11: [ RUN ] PathTest.StripSourcePrefixWorks 11: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 11: [----------] 1 test from PathTest (0 ms total) 11: 11: [----------] 2 tests from PhysicalNodeCommunicatorTest 11: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 11: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 11: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 11: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 11: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 11: 11: [----------] 5 tests from Range 11: [ RUN ] Range.EmptyRangeWorks 11: [ OK ] Range.EmptyRangeWorks (0 ms) 11: [ RUN ] Range.NonEmptyRangeWorks 11: [ OK ] Range.NonEmptyRangeWorks (0 ms) 11: [ RUN ] Range.BeginEnd 11: [ OK ] Range.BeginEnd (0 ms) 11: [ RUN ] Range.IsInRangeWorks 11: [ OK ] Range.IsInRangeWorks (0 ms) 11: [ RUN ] Range.IteratorWorks 11: [ OK ] Range.IteratorWorks (0 ms) 11: [----------] 5 tests from Range (0 ms total) 11: 11: [----------] 7 tests from StringConvert 11: [ RUN ] StringConvert.NoResultFromEptyString 11: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 11: [ RUN ] StringConvert.ThreeFloatsSuccessfully 11: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 11: [ RUN ] StringConvert.OneIntSucessfully 11: [ OK ] StringConvert.OneIntSucessfully (0 ms) 11: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 11: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 11: [ RUN ] StringConvert.ThrowsWhenWrongSize 11: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 11: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 11: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 11: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 11: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 11: [----------] 7 tests from StringConvert (0 ms total) 11: 11: [----------] 7 tests from StringToEnumValueConverterTest 11: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 11: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 11: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 11: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 11: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 11: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 11: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 11: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 11: [----------] 7 tests from StringToEnumValueConverterTest (4 ms total) 11: 11: [----------] 9 tests from StringUtilityTest 11: [ RUN ] StringUtilityTest.StartsWith 11: [ OK ] StringUtilityTest.StartsWith (0 ms) 11: [ RUN ] StringUtilityTest.EndsWith 11: [ OK ] StringUtilityTest.EndsWith (0 ms) 11: [ RUN ] StringUtilityTest.StripSuffixIfPresent 11: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 11: [ RUN ] StringUtilityTest.StripString 11: [ OK ] StringUtilityTest.StripString (0 ms) 11: [ RUN ] StringUtilityTest.SplitString 11: [ OK ] StringUtilityTest.SplitString (0 ms) 11: [ RUN ] StringUtilityTest.SplitDelimitedString 11: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 11: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 11: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 11: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 11: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 11: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 11: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 11: [----------] 9 tests from StringUtilityTest (0 ms total) 11: 11: [----------] 2 tests from FormatStringTest 11: [ RUN ] FormatStringTest.HandlesBasicFormatting 11: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 11: [ RUN ] FormatStringTest.HandlesLongStrings 11: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 11: [----------] 2 tests from FormatStringTest (0 ms total) 11: 11: [----------] 1 test from StringFormatterTest 11: [ RUN ] StringFormatterTest.HandlesBasicFormatting 11: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 11: [----------] 1 test from StringFormatterTest (0 ms total) 11: 11: [----------] 1 test from formatAndJoinTest 11: [ RUN ] formatAndJoinTest.Works 11: [ OK ] formatAndJoinTest.Works (0 ms) 11: [----------] 1 test from formatAndJoinTest (0 ms total) 11: 11: [----------] 1 test from JoinStringsTest 11: [ RUN ] JoinStringsTest.Works 11: [ OK ] JoinStringsTest.Works (0 ms) 11: [----------] 1 test from JoinStringsTest (0 ms total) 11: 11: [----------] 6 tests from ReplaceAllTest 11: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 11: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesNoMatches 11: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 11: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 11: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 11: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 11: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 11: [----------] 6 tests from ReplaceAllTest (0 ms total) 11: 11: [----------] 10 tests from TextLineWrapperTest 11: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 11: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 11: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 11: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 11: [ RUN ] TextLineWrapperTest.WrapsCorrectly 11: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 11: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 11: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesIndent 11: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 11: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 11: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 11: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 11: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 11: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 11: [----------] 10 tests from TextLineWrapperTest (0 ms total) 11: 11: [----------] 3 tests from TemplateMPTest 11: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 11: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 11: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 11: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 11: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 11: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 11: [----------] 3 tests from TemplateMPTest (0 ms total) 11: 11: [----------] 6 tests from TextWriterTest 11: [ RUN ] TextWriterTest.WritesLines 11: [ OK ] TextWriterTest.WritesLines (0 ms) 11: [ RUN ] TextWriterTest.WritesLinesInParts 11: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 11: [ RUN ] TextWriterTest.WritesWrappedLines 11: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 11: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 11: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 11: [ RUN ] TextWriterTest.TracksNewlines 11: [ OK ] TextWriterTest.TracksNewlines (0 ms) 11: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 11: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 11: [----------] 6 tests from TextWriterTest (0 ms total) 11: 11: [----------] 1 test from TypeTraitsTest 11: [ RUN ] TypeTraitsTest.IsIntegralConstant 11: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 11: [----------] 1 test from TypeTraitsTest (0 ms total) 11: 11: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 11: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 11: 11: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 11: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 11: 11: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 11: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 11: 11: [----------] 11 tests from WithInputPaths/PathSearchTest 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 11: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 11: 11: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 11: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 386 tests from 61 test suites ran. (28 ms total) 11: [ PASSED ] 386 tests. 11: 11: YOU HAVE 1 DISABLED TEST 11: 11/81 Test #11: UtilityUnitTests ............................... Passed 0.14 sec test 12 Start 12: UtilityMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/utility/tests 12: Test timeout computed to be: 30 12: [==========] Running 2 tests from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 2 tests from PhysicalNodeCommunicatorTest 12: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 12: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (27 ms) 12: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 12: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (27 ms) 12: [----------] 2 tests from PhysicalNodeCommunicatorTest (55 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 2 tests from 1 test suite ran. (60 ms total) 12: [ PASSED ] 2 tests. 12/81 Test #12: UtilityMpiUnitTests ............................ Passed 0.10 sec test 13 Start 13: GmxlibTests 13: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/GmxlibTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests 13: Test timeout computed to be: 30 13: [==========] Running 72 tests from 1 test suite. 13: [----------] Global test environment set-up. 13: [----------] 72 tests from NBInteraction/NonbondedFepTest 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (4 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (8 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (8 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 13: [----------] 72 tests from NBInteraction/NonbondedFepTest (33 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 72 tests from 1 test suite ran. (33 ms total) 13: [ PASSED ] 72 tests. 13/81 Test #13: GmxlibTests .................................... Passed 0.13 sec test 14 Start 14: MdlibUnitTest 14: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 14: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests 14: Test timeout computed to be: 30 14: [==========] Running 155 tests from 17 test suites. 14: [----------] Global test environment set-up. 14: [----------] 1 test from VerletBufferConstraintTest 14: [ RUN ] VerletBufferConstraintTest.EqualMasses 14: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 14: [----------] 1 test from VerletBufferConstraintTest (4 ms total) 14: 14: [----------] 6 tests from CalcvirTest 14: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 14: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 14: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 14: [----------] 6 tests from CalcvirTest (0 ms total) 14: 14: [----------] 2 tests from PrEbinTest 14: [ RUN ] PrEbinTest.HandlesAverages 14: [ OK ] PrEbinTest.HandlesAverages (0 ms) 14: [ RUN ] PrEbinTest.HandlesEmptyAverages 14: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 14: [----------] 2 tests from PrEbinTest (0 ms total) 14: 14: [----------] 3 tests from EnergyDriftTracker 14: [ RUN ] EnergyDriftTracker.emptyWorks 14: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 14: [ RUN ] EnergyDriftTracker.onePointWorks 14: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 14: [ RUN ] EnergyDriftTracker.manyPointsWorks 14: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 14: [----------] 3 tests from EnergyDriftTracker (0 ms total) 14: 14: [----------] 4 tests from ShakeTest 14: [ RUN ] ShakeTest.ConstrainsOneBond 14: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 14: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 14: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 14: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 14: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 14: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 14: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 14: [----------] 4 tests from ShakeTest (0 ms total) 14: 14: [----------] 1 test from NullSignalTest 14: [ RUN ] NullSignalTest.NullSignallerWorks 14: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 14: [----------] 1 test from NullSignalTest (0 ms total) 14: 14: [----------] 7 tests from SignalTest 14: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 14: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 14: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 14: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 14: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 14: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 14: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 14: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 14: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 14: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 14: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 14: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 14: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 14: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 14: [----------] 7 tests from SignalTest (0 ms total) 14: 14: [----------] 13 tests from UpdateGroupsTest 14: [ RUN ] UpdateGroupsTest.WithEthaneUA 14: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 14: [ RUN ] UpdateGroupsTest.WithMethane 14: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 14: [ RUN ] UpdateGroupsTest.WithEthane 14: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 14: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 14: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 14: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 14: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 14: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 14: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 14: [ RUN ] UpdateGroupsTest.WithWaterFourSite 14: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 14: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 14: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 14: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 14: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 14: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 14: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 14: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 14: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 14: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 14: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 14: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 14: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 14: [----------] 13 tests from UpdateGroupsTest (1 ms total) 14: 14: [----------] 1 test from UpdateGroupsCog 14: [ RUN ] UpdateGroupsCog.ComputesCogs 14: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 14: [----------] 1 test from UpdateGroupsCog (0 ms total) 14: 14: [----------] 2 tests from WholeMoleculeTransform 14: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 14: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 14: [ RUN ] WholeMoleculeTransform.HandlesReordering 14: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 14: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 14: 14: [----------] 14 tests from WithParameters/ConstraintsTest 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (4 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (29 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (32 ms) 14: [----------] 14 tests from WithParameters/ConstraintsTest (81 ms total) 14: 14: [----------] 11 tests from WithParameters/EnergyOutputTest 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (2 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (5 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (8 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 14: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file 14: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (43 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (7 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (5 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (2 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (6 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (7 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 14: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (2 ms) 14: [----------] 11 tests from WithParameters/EnergyOutputTest (95 ms total) 14: 14: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 14: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 14: 14: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 14: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 14: 14: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 14: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 14: 14: [----------] 16 tests from WithParameters/LeapFrogTest 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (11 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (39 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (8 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (5 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (11 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (11 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (7 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (7 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (7 ms) 14: [----------] 16 tests from WithParameters/LeapFrogTest (116 ms total) 14: 14: [----------] 13 tests from WithParameters/SettleTest 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (4 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (12 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (7 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (1 ms) 14: [----------] 13 tests from WithParameters/SettleTest (32 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 155 tests from 17 test suites ran. (335 ms total) 14: [ PASSED ] 155 tests. 14/81 Test #14: MdlibUnitTest .................................. Passed 0.57 sec test 15 Start 15: AwhTest 15: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/AwhTest.xml" 15: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/awh/tests 15: Test timeout computed to be: 30 15: [==========] Running 21 tests from 8 test suites. 15: [----------] Global test environment set-up. 15: [----------] 3 tests from SerializationTest 15: [ RUN ] SerializationTest.CanSerializeDimParams 15: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 15: [ RUN ] SerializationTest.CanSerializeBiasParams 15: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 15: [ RUN ] SerializationTest.CanSerializeAwhParams 15: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 15: [----------] 3 tests from SerializationTest (0 ms total) 15: 15: [----------] 1 test from BiasTest 15: [ RUN ] BiasTest.DetectsCovering 15: [ OK ] BiasTest.DetectsCovering (0 ms) 15: [----------] 1 test from BiasTest (0 ms total) 15: 15: [----------] 1 test from biasGridTest 15: [ RUN ] biasGridTest.neighborhood 15: [ OK ] biasGridTest.neighborhood (1 ms) 15: [----------] 1 test from biasGridTest (1 ms total) 15: 15: [----------] 1 test from BiasSharingTest 15: [ RUN ] BiasSharingTest.SharingWorks 15: [ OK ] BiasSharingTest.SharingWorks (117 ms) 15: [----------] 1 test from BiasSharingTest (117 ms total) 15: 15: [----------] 1 test from BiasFepLambdaStateTest 15: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 15: [ OK ] BiasFepLambdaStateTest.DetectsCovering (3 ms) 15: [----------] 1 test from BiasFepLambdaStateTest (3 ms total) 15: 15: [----------] 8 tests from WithParameters/BiasTest 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms) 15: [----------] 8 tests from WithParameters/BiasTest (3 ms total) 15: 15: [----------] 2 tests from WithParameters/BiasStateTest 15: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 15: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 15: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 15: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 15: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 15: 15: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (8 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (7 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (7 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (7 ms) 15: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (33 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 21 tests from 8 test suites ran. (161 ms total) 15: [ PASSED ] 21 tests. 15/81 Test #15: AwhTest ........................................ Passed 0.20 sec test 16 Start 16: DensityFittingAppliedForcesUnitTest 16: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests 16: Test timeout computed to be: 30 16: [==========] Running 18 tests from 4 test suites. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from DensityFittingTest 16: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 16: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 16: [ RUN ] DensityFittingTest.SingleAtom 16: [ OK ] DensityFittingTest.SingleAtom (0 ms) 16: [----------] 2 tests from DensityFittingTest (0 ms total) 16: 16: [----------] 7 tests from DensityFittingAmplitudeLookupTest 16: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 16: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 16: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 16: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 16: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 16: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 16: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 16: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 16: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 16: 16: [----------] 1 test from DensityFittingForceProviderState 16: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 16: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 16: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 16: 16: [----------] 8 tests from DensityFittingOptionsTest 16: [ RUN ] DensityFittingOptionsTest.DefaultParameters 16: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 16: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 16: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 16: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 16: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 16: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 16: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 16: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 16: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 16: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 16: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 16: [ RUN ] DensityFittingOptionsTest.KvtToInternal 16: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 16: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 16: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 16: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 18 tests from 4 test suites ran. (1 ms total) 16: [ PASSED ] 18 tests. 16/81 Test #16: DensityFittingAppliedForcesUnitTest ............ Passed 0.02 sec test 17 Start 17: QMMMAppliedForcesUnitTest 17: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests 17: Test timeout computed to be: 30 17: [==========] Running 21 tests from 5 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from QMMMInputGeneratorTest 17: [ RUN ] QMMMInputGeneratorTest.CanConstruct 17: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 17: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 17: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 17: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 17: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 17: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 17: 17: [----------] 7 tests from QMMMTopologyPreprocessorTest 17: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 17: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 21.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Setting the LD random seed to -806356137 17: 17: Generated 10 of the 10 non-bonded parameter combinations 17: 17: Generated 10 of the 10 1-4 parameter combinations 17: 17: Excluding 2 bonded neighbours molecule type 'SOL' 17: Analysing residue names: 17: There are: 4 Water residues 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (14 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 21.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Setting the LD random seed to -687868229 17: 17: Generated 10 of the 10 non-bonded parameter combinations 17: 17: Generated 10 of the 10 1-4 parameter combinations 17: 17: Excluding 2 bonded neighbours molecule type 'SOL' 17: Analysing residue names: 17: There are: 4 Water residues 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (14 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 21.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Setting the LD random seed to 2045734351 17: 17: Generated 10 of the 10 non-bonded parameter combinations 17: 17: Generated 10 of the 10 1-4 parameter combinations 17: 17: Excluding 2 bonded neighbours molecule type 'SOL' 17: Analysing residue names: 17: There are: 4 Water residues 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (9 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 63.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 17: NVE simulation: will use the initial temperature of 129.093 K for 17: determining the Verlet buffer size 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Setting the LD random seed to -41005 17: 17: Generated 2145 of the 2145 non-bonded parameter combinations 17: 17: Generated 2145 of the 2145 1-4 parameter combinations 17: 17: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 17: Analysing residue names: 17: There are: 3 Protein residues 17: Analysing Protein... 17: 17: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 17: 17: Calculated rlist for 1x1 atom pair-list as 1.013 nm, buffer size 0.013 nm 17: 17: Set rlist, assuming 4x4 atom pair-list, to 1.008 nm, buffer size 0.008 nm 17: 17: Note that mdrun will redetermine rlist based on the actual pair-list setup 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (47 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: 17: NOTE 2 [file unknown]: 17: You are using constraints on all bonds, whereas the forcefield has been 17: parametrized only with constraints involving hydrogen atoms. We suggest 17: using constraints = h-bonds instead, this will also improve performance. 17: 17: 17: NOTE 3 [file unknown]: 17: For energy conservation with LINCS, lincs_iter should be 2 or larger. 17: 17: 17: Number of degrees of freedom in T-Coupling group rest is 42.00 17: 17: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 17: NVE simulation: will use the initial temperature of 193.640 K for 17: determining the Verlet buffer size 17: 17: 17: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 5 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Setting the LD random seed to 1768791031 17: 17: Generated 2145 of the 2145 non-bonded parameter combinations 17: 17: Generated 2145 of the 2145 1-4 parameter combinations 17: 17: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 17: 17: turning all bonds into constraints... 17: Analysing residue names: 17: There are: 3 Protein residues 17: Analysing Protein... 17: 17: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 17: 17: Calculated rlist for 1x1 atom pair-list as 1.015 nm, buffer size 0.015 nm 17: 17: Set rlist, assuming 4x4 atom pair-list, to 1.009 nm, buffer size 0.009 nm 17: 17: Note that mdrun will redetermine rlist based on the actual pair-list setup 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (48 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Number of degrees of freedom in T-Coupling group rest is 45.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 17: Setting the LD random seed to -1103434038 17: 17: Generated 3 of the 6 non-bonded parameter combinations 17: 17: Excluding 3 bonded neighbours molecule type 'VSTEST' 17: 17: Cleaning up constraints and constant bonded interactions with virtual sites 17: Analysing residue names: 17: There are: 1 Other residues 17: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (14 ms) 17: [----------] 7 tests from QMMMTopologyPreprocessorTest (149 ms total) 17: 17: [----------] 9 tests from QMMMOptionsTest 17: [ RUN ] QMMMOptionsTest.DefaultParameters 17: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 17: [ RUN ] QMMMOptionsTest.OptionSetsActive 17: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 17: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 17: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 17: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 17: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 17: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 17: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 17: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 17: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 17: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 17: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 17: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 17: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 17: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 17: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 17: [----------] 9 tests from QMMMOptionsTest (1 ms total) 17: 17: [----------] 1 test from QMMMForceProviderTest 17: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 17: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 17: [----------] 1 test from QMMMForceProviderTest (0 ms total) 17: 17: [----------] 1 test from QMMMTest 17: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 17: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 17: [----------] 1 test from QMMMTest (0 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 21 tests from 5 test suites ran. (152 ms total) 17: [ PASSED ] 21 tests. 17/81 Test #17: QMMMAppliedForcesUnitTest ...................... Passed 0.21 sec test 18 Start 18: AppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/applied_forces/tests 18: Test timeout computed to be: 30 18: [==========] Running 3 tests from 1 test suite. 18: [----------] Global test environment set-up. 18: [----------] 3 tests from ElectricFieldTest 18: [ RUN ] ElectricFieldTest.Static 18: [ OK ] ElectricFieldTest.Static (0 ms) 18: [ RUN ] ElectricFieldTest.Oscillating 18: [ OK ] ElectricFieldTest.Oscillating (0 ms) 18: [ RUN ] ElectricFieldTest.Pulsed 18: [ OK ] ElectricFieldTest.Pulsed (0 ms) 18: [----------] 3 tests from ElectricFieldTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 3 tests from 1 test suite ran. (0 ms total) 18: [ PASSED ] 3 tests. 18/81 Test #18: AppliedForcesUnitTest .......................... Passed 0.04 sec test 19 Start 19: ListedForcesTest 19: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/listed_forces/tests 19: Test timeout computed to be: 30 19: [==========] Running 132 tests from 9 test suites. 19: [----------] Global test environment set-up. 19: [----------] 24 tests from Bond/ListedForcesTest 19: [ RUN ] Bond/ListedForcesTest.Ifunc/0 19: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/1 19: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/2 19: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/3 19: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/4 19: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/5 19: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/6 19: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/7 19: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/8 19: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/9 19: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/10 19: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/11 19: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/12 19: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/13 19: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/14 19: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/15 19: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/16 19: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/17 19: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/18 19: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/19 19: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/20 19: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/21 19: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/22 19: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/23 19: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 19: [----------] 24 tests from Bond/ListedForcesTest (4 ms total) 19: 19: [----------] 33 tests from Angle/ListedForcesTest 19: [ RUN ] Angle/ListedForcesTest.Ifunc/0 19: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/1 19: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/2 19: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/3 19: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/4 19: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/5 19: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/6 19: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/7 19: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/8 19: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/9 19: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/10 19: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/11 19: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/12 19: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/13 19: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/14 19: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/15 19: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/16 19: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/17 19: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/18 19: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/19 19: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/20 19: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/21 19: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/22 19: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/23 19: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/24 19: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/25 19: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/26 19: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/27 19: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/28 19: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/29 19: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/30 19: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/31 19: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/32 19: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 19: [----------] 33 tests from Angle/ListedForcesTest (5 ms total) 19: 19: [----------] 18 tests from Dihedral/ListedForcesTest 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 19: [----------] 18 tests from Dihedral/ListedForcesTest (3 ms total) 19: 19: [----------] 12 tests from Polarize/ListedForcesTest 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 19: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 19: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 19: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 19: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 19: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 19: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 19: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 19: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 19: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 19: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 19: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 19: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 19: [----------] 12 tests from Polarize/ListedForcesTest (1 ms total) 19: 19: [----------] 18 tests from Restraints/ListedForcesTest 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 19: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 19: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 19: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 19: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 19: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 19: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 19: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 19: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 19: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 19: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 19: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 19: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 19: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 19: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 19: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 19: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 19: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 19: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 19: [----------] 18 tests from Restraints/ListedForcesTest (3 ms total) 19: 19: [----------] 3 tests from BondZeroLength/ListedForcesTest 19: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 19: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 19: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 19: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 19: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 19: 19: [----------] 3 tests from AngleZero/ListedForcesTest 19: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 19: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 19: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 19: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 19: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 19: 19: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 19: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (2 ms total) 19: 19: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 19: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (1 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 132 tests from 9 test suites ran. (22 ms total) 19: [ PASSED ] 132 tests. 19/81 Test #19: ListedForcesTest ............................... Passed 0.10 sec test 20 Start 20: NbnxmTests 20: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/NbnxmTests.xml" 20: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/nbnxm/tests 20: Test timeout computed to be: 30 20: [==========] Running 18 tests from 1 test suite. 20: [----------] Global test environment set-up. 20: [----------] 18 tests from KernelSetupTest 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 20: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 20: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 20: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 20: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 20: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 20: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 20: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 20: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 20: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 20: [----------] 18 tests from KernelSetupTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 18 tests from 1 test suite ran. (0 ms total) 20: [ PASSED ] 18 tests. 20/81 Test #20: NbnxmTests ..................................... Passed 0.05 sec test 21 Start 21: CommandLineUnitTests 21: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 21: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/commandline/tests 21: Test timeout computed to be: 30 21: [==========] Running 60 tests from 7 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from CommandLineHelpModuleTest 21: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 21: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 21: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 21: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 21: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 21: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 21: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) 21: 21: [----------] 7 tests from CommandLineHelpWriterTest 21: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 21: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 21: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 21: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 21: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 21: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 21: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 21: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 21: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) 21: 21: [----------] 6 tests from CommandLineModuleManagerTest 21: [ RUN ] CommandLineModuleManagerTest.RunsModule 21: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 21: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (4 ms) 21: [----------] 6 tests from CommandLineModuleManagerTest (5 ms total) 21: 21: [----------] 13 tests from CommandLineParserTest 21: [ RUN ] CommandLineParserTest.HandlesSingleValues 21: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 21: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 21: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 21: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 21: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 21: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesString 21: [ OK ] CommandLineParserTest.HandlesString (0 ms) 21: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 21: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 21: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 21: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 21: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 21: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 21: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 21: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 21: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 21: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 21: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 21: [----------] 13 tests from CommandLineParserTest (0 ms total) 21: 21: [----------] 6 tests from CommandLineProgramContextTest 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 21: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 21: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 21: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 21: 21: [----------] 3 tests from OutputNamesTest 21: [ RUN ] OutputNamesTest.CanBeSuffixed 21: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 21: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 21: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 21: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 21: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 21: [----------] 3 tests from OutputNamesTest (0 ms total) 21: 21: [----------] 22 tests from ParseCommonArgsTest 21: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 21: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 21: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 21: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 21: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 21: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 21: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 21: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 21: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 21: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 21: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 21: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 21: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 21: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 21: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 21: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 21: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 21: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 21: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 21: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 21: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 21: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 21: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 21: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 21: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 21: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 21: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 21: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 21: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 21: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 21: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 21: [----------] 22 tests from ParseCommonArgsTest (1 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 60 tests from 7 test suites ran. (11 ms total) 21: [ PASSED ] 60 tests. 21/81 Test #21: CommandLineUnitTests ........................... Passed 0.05 sec test 22 Start 22: DomDecTests 22: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/DomDecTests.xml" 22: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests 22: Test timeout computed to be: 30 22: [==========] Running 9 tests from 2 test suites. 22: [----------] Global test environment set-up. 22: [----------] 7 tests from HashedMap 22: [ RUN ] HashedMap.InsertsFinds 22: [ OK ] HashedMap.InsertsFinds (0 ms) 22: [ RUN ] HashedMap.NegativeKeysWork 22: [ OK ] HashedMap.NegativeKeysWork (0 ms) 22: [ RUN ] HashedMap.InsertsErases 22: [ OK ] HashedMap.InsertsErases (0 ms) 22: [ RUN ] HashedMap.InsertsOrAssigns 22: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 22: [ RUN ] HashedMap.Clears 22: [ OK ] HashedMap.Clears (0 ms) 22: [ RUN ] HashedMap.LinkedEntries 22: [ OK ] HashedMap.LinkedEntries (0 ms) 22: [ RUN ] HashedMap.ResizesTable 22: [ OK ] HashedMap.ResizesTable (0 ms) 22: [----------] 7 tests from HashedMap (0 ms total) 22: 22: [----------] 2 tests from LocalAtomSetManager 22: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 22: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 22: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 22: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 22: [----------] 2 tests from LocalAtomSetManager (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 9 tests from 2 test suites ran. (0 ms total) 22: [ PASSED ] 9 tests. 22/81 Test #22: DomDecTests .................................... Passed 0.04 sec test 23 Start 23: DomDecMpiTests 23: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml" 23: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/domdec/tests 23: Test timeout computed to be: 30 23: [==========] Running 4 tests from 1 test suite. 23: [----------] Global test environment set-up. 23: [----------] 4 tests from HaloExchangeTest 23: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 23: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (31 ms) 23: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 23: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (27 ms) 23: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 23: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (27 ms) 23: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 23: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (31 ms) 23: [----------] 4 tests from HaloExchangeTest (119 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 4 tests from 1 test suite ran. (119 ms total) 23: [ PASSED ] 4 tests. 23/81 Test #23: DomDecMpiTests ................................. Passed 0.30 sec test 24 Start 24: EwaldUnitTests 24: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/ewald/tests 24: Test timeout computed to be: 30 24: [==========] Running 407 tests from 9 test suites. 24: [----------] Global test environment set-up. 24: [----------] 6 tests from SeparatePmeRanksPermittedTest 24: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 24: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 24: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 24: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 24: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 24: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 24: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 24: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 24: 24: [----------] 108 tests from Pme_SplineAndSpreadTest 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (278 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (4 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (7 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (9 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (4 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (10 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (9 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (6 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (9 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (6 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (7 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (7 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (9 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (5 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (7 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (9 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (4 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (12 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (4 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (8 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (8 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (10 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (10 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (6 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (4 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (4 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (4 ms) 24: [----------] 108 tests from Pme_SplineAndSpreadTest (639 ms total) 24: 24: [----------] 64 tests from Pme_SolveTest 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (2 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [----------] 64 tests from Pme_SolveTest (32 ms total) 24: 24: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (10 ms total) 24: 24: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (17 ms total) 24: 24: [----------] 64 tests from PmeDiffEps_SolveTest 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [----------] 64 tests from PmeDiffEps_SolveTest (27 ms total) 24: 24: [----------] 72 tests from Pme_GatherTest 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [----------] 72 tests from Pme_GatherTest (30 ms total) 24: 24: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (4 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 24: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (4 ms total) 24: 24: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (5 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (4 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (8 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (3 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (4 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (5 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (3 ms) 24: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (82 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 407 tests from 9 test suites ran. (845 ms total) 24: [ PASSED ] 311 tests. 24: [ SKIPPED ] 96 tests, listed below: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24/81 Test #24: EwaldUnitTests ................................. Passed 1.10 sec test 25 Start 25: FFTUnitTests 25: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fft/tests 25: Test timeout computed to be: 1920 25: [==========] Running 15 tests from 4 test suites. 25: [----------] Global test environment set-up. 25: [----------] 2 tests from ManyFFTTest 25: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 25: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (41 ms) 25: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 25: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (75 ms) 25: [----------] 2 tests from ManyFFTTest (126 ms total) 25: 25: [----------] 1 test from FFTTest 25: [ RUN ] FFTTest.Real2DLength18_15Test 25: [ OK ] FFTTest.Real2DLength18_15Test (18 ms) 25: [----------] 1 test from FFTTest (18 ms total) 25: 25: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (5 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (10 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (11 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (13 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (47 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (36 ms) 25: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (130 ms total) 25: 25: [----------] 2 tests from Works/ParameterizedFFTTest3D 25: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 25: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (2 ms) 25: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 25: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (12 ms) 25: [----------] 2 tests from Works/ParameterizedFFTTest3D (15 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 15 tests from 4 test suites ran. (291 ms total) 25: [ PASSED ] 15 tests. 25/81 Test #25: FFTUnitTests ................................... Passed 0.47 sec test 26 Start 26: GpuUtilsUnitTests 26: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gpu_utils/tests 26: Test timeout computed to be: 30 26: [==========] Running 64 tests from 22 test suites. 26: [----------] Global test environment set-up. 26: [----------] 2 tests from ClfftInitializer 26: [ RUN ] ClfftInitializer.SingleInitializationWorks 26: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 26: [ RUN ] ClfftInitializer.TwoInitializationsWork 26: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 26: [----------] 2 tests from ClfftInitializer (0 ms total) 26: 26: [----------] 1 test from DevicesAvailable 26: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 26: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 26: [----------] 1 test from DevicesAvailable (0 ms total) 26: 26: [----------] 1 test from DeviceStreamManagerTest 26: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 26: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 26: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 26: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 26: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 26: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 26: 26: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 26: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 26: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 26: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 26: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 26: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 26: 26: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 26: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 26: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 26: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 26: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 26: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 26: 26: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 26: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 26: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 26: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 26: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 26: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 26: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.Swap 26: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.Comparison 26: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 26: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 26: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.Swap 26: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.Comparison 26: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 26: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.Swap 26: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.Comparison 26: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 26: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 26: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.Swap 26: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.Comparison 26: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 26: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 26: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 26: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 26: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 26: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 26: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 26: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 26: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 26: 26: [----------] 1 test from HostAllocatorUntypedTest 26: [ RUN ] HostAllocatorUntypedTest.Comparison 26: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 26: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 26: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/0.Move 26: [ OK ] AllocatorTest/0.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/0 (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 26: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/1.Move 26: [ OK ] AllocatorTest/1.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/1 (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 26: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/2.Move 26: [ OK ] AllocatorTest/2.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/2 (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 26: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/3.Move 26: [ OK ] AllocatorTest/3.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/3 (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 64 tests from 22 test suites ran. (2 ms total) 26: [ PASSED ] 64 tests. 26/81 Test #26: GpuUtilsUnitTests .............................. Passed 0.19 sec test 27 Start 27: HardwareUnitTests 27: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/hardware/tests 27: Test timeout computed to be: 30 27: [==========] Running 21 tests from 9 test suites. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CpuInfoTest 27: [ RUN ] CpuInfoTest.SupportLevel 27: [ OK ] CpuInfoTest.SupportLevel (35 ms) 27: [----------] 1 test from CpuInfoTest (35 ms total) 27: 27: [----------] 4 tests from HardwareTopologyTest 27: [ RUN ] HardwareTopologyTest.Execute 27: [ OK ] HardwareTopologyTest.Execute (113 ms) 27: [ RUN ] HardwareTopologyTest.HwlocExecute 27: [ OK ] HardwareTopologyTest.HwlocExecute (107 ms) 27: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 27: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (123 ms) 27: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 27: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (147 ms) 27: [----------] 4 tests from HardwareTopologyTest (493 ms total) 27: 27: [----------] 1 test from DevicesManagerTest 27: [ RUN ] DevicesManagerTest.Serialization 27: [ OK ] DevicesManagerTest.Serialization (0 ms) 27: [----------] 1 test from DevicesManagerTest (0 ms total) 27: 27: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (6 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 27: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (22 ms total) 27: 27: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (25 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (6 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 27: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (35 ms total) 27: 27: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 27: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 27: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (12 ms) 27: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 27: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 27: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (14 ms total) 27: 27: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 27: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (154 ms) 27: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (155 ms total) 27: 27: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 27: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (143 ms) 27: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (143 ms total) 27: 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 27: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (232 ms) 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (232 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 21 tests from 9 test suites ran. (1132 ms total) 27: [ PASSED ] 21 tests. 27/81 Test #27: HardwareUnitTests .............................. Passed 1.16 sec test 28 Start 28: MathUnitTests 28: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/math/tests 28: Test timeout computed to be: 30 28: [==========] Running 301 tests from 38 test suites. 28: [----------] Global test environment set-up. 28: [----------] 1 test from EmptyArrayRefWithPaddingTest 28: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 28: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 28: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 28: 28: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 28: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 28: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 28: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 28: 28: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 28: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 28: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 28: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 28: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 28: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 28: 28: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 28: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 28: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 28: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 28: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 28: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 28: 28: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 28: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 28: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 28: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 28: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 28: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 28: 28: [----------] 11 tests from TranslateAndScaleTest 28: [ RUN ] TranslateAndScaleTest.identityTransformation 28: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 28: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 28: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 28: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 28: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 28: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 28: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 28: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingIdentity 28: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 28: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 28: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 28: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 28: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 28: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 28: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 28: 28: [----------] 3 tests from AffineTransformationTest 28: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 28: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 28: [ RUN ] AffineTransformationTest.applyTransformationToVectors 28: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 28: [ RUN ] AffineTransformationTest.retrieveGradient 28: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 28: [----------] 3 tests from AffineTransformationTest (0 ms total) 28: 28: [----------] 12 tests from DensitySimilarityTest 28: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 28: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 28: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 28: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 28: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 28: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 28: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 28: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 28: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 28: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 28: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 28: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 28: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (46 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (37 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (3 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 28: [----------] 12 tests from DensitySimilarityTest (87 ms total) 28: 28: [----------] 6 tests from StructureSimilarityTest 28: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 28: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 28: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 28: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 28: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 28: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 28: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 28: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 28: [----------] 6 tests from StructureSimilarityTest (0 ms total) 28: 28: [----------] 8 tests from ExponentialMovingAverage 28: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 28: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 28: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 28: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 28: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 28: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 28: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 28: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 28: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 28: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 28: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 28: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 28: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 28: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 28: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 28: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 28: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 28: 28: [----------] 21 tests from FunctionTest 28: [ RUN ] FunctionTest.StaticLog2 28: [ OK ] FunctionTest.StaticLog2 (0 ms) 28: [ RUN ] FunctionTest.Log2I32Bit 28: [ OK ] FunctionTest.Log2I32Bit (0 ms) 28: [ RUN ] FunctionTest.Log2I64Bit 28: [ OK ] FunctionTest.Log2I64Bit (0 ms) 28: [ RUN ] FunctionTest.GreatestCommonDivisor 28: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 28: [ RUN ] FunctionTest.InvsqrtFloat 28: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 28: [ RUN ] FunctionTest.InvsqrtDouble 28: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 28: [ RUN ] FunctionTest.InvsqrtInteger 28: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 28: [ RUN ] FunctionTest.InvcbrtFloat 28: [ OK ] FunctionTest.InvcbrtFloat (6 ms) 28: [ RUN ] FunctionTest.InvcbrtDouble 28: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 28: [ RUN ] FunctionTest.InvcbrtInteger 28: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 28: [ RUN ] FunctionTest.SixthrootFloat 28: [ OK ] FunctionTest.SixthrootFloat (0 ms) 28: [ RUN ] FunctionTest.SixthrootDouble 28: [ OK ] FunctionTest.SixthrootDouble (0 ms) 28: [ RUN ] FunctionTest.SixthrootInteger 28: [ OK ] FunctionTest.SixthrootInteger (0 ms) 28: [ RUN ] FunctionTest.InvsixthrootFloat 28: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 28: [ RUN ] FunctionTest.InvsixthrootDouble 28: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 28: [ RUN ] FunctionTest.InvsixthrootInteger 28: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 28: [ RUN ] FunctionTest.Powers 28: [ OK ] FunctionTest.Powers (0 ms) 28: [ RUN ] FunctionTest.ErfInvFloat 28: [ OK ] FunctionTest.ErfInvFloat (0 ms) 28: [ RUN ] FunctionTest.ErfInvDouble 28: [ OK ] FunctionTest.ErfInvDouble (0 ms) 28: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 28: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 28: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 28: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 28: [----------] 21 tests from FunctionTest (8 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/0, where TypeParam = char 28: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/0 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 28: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/1 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/2, where TypeParam = int 28: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/2 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/3, where TypeParam = unsigned int 28: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/3 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/4, where TypeParam = long 28: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/4 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/5, where TypeParam = unsigned long 28: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/5 (0 ms total) 28: 28: [----------] 4 tests from GaussianOn1DLattice 28: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 28: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 28: [ RUN ] GaussianOn1DLattice.isCorrect 28: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 28: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 28: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 28: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 28: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 28: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 28: 28: [----------] 9 tests from GaussTransformTest 28: [ RUN ] GaussTransformTest.isZeroUponConstruction 28: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 28: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 28: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 28: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 28: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 28: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 28: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 28: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 28: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 28: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 28: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 28: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 28: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 28: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 28: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 28: [ RUN ] GaussTransformTest.view 28: [ OK ] GaussTransformTest.view (0 ms) 28: [----------] 9 tests from GaussTransformTest (0 ms total) 28: 28: [----------] 3 tests from DensityFittingForce 28: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 28: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 28: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 28: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 28: [ RUN ] DensityFittingForce.pullsTowardsDerivative 28: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 28: [----------] 3 tests from DensityFittingForce (0 ms total) 28: 28: [----------] 2 tests from InvertMatrixTest 28: [ RUN ] InvertMatrixTest.IdentityIsImpotent 28: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 28: [ RUN ] InvertMatrixTest.ComputesInverse 28: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 28: [----------] 2 tests from InvertMatrixTest (0 ms total) 28: 28: [----------] 2 tests from InvertBoxMatrixTest 28: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 28: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 28: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 28: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 28: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 28: 28: [----------] 17 tests from MatrixTest 28: [ RUN ] MatrixTest.canSetFromArray 28: [ OK ] MatrixTest.canSetFromArray (0 ms) 28: [ RUN ] MatrixTest.canSetStaticallyFromList 28: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 28: [ RUN ] MatrixTest.canConstructAndFill 28: [ OK ] MatrixTest.canConstructAndFill (0 ms) 28: [ RUN ] MatrixTest.canSetValues 28: [ OK ] MatrixTest.canSetValues (0 ms) 28: [ RUN ] MatrixTest.canCopyAssign 28: [ OK ] MatrixTest.canCopyAssign (0 ms) 28: [ RUN ] MatrixTest.canSwap 28: [ OK ] MatrixTest.canSwap (0 ms) 28: [ RUN ] MatrixTest.staticMultiDimArrayExtent 28: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 28: [ RUN ] MatrixTest.determinantWorks 28: [ OK ] MatrixTest.determinantWorks (0 ms) 28: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 28: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 28: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 28: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 28: [ RUN ] MatrixTest.traceWorks 28: [ OK ] MatrixTest.traceWorks (0 ms) 28: [ RUN ] MatrixTest.transposeWorks 28: [ OK ] MatrixTest.transposeWorks (0 ms) 28: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 28: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 28: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 28: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 28: [ RUN ] MatrixTest.canFillLegacyMatrix 28: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 28: [ RUN ] MatrixTest.IdentityMatrix 28: [ OK ] MatrixTest.IdentityMatrix (0 ms) 28: [ RUN ] MatrixTest.MatrixVectorMultiplication 28: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 28: [----------] 17 tests from MatrixTest (0 ms total) 28: 28: [----------] 25 tests from MultiDimArrayTest 28: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 28: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 28: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 28: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 28: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 28: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 28: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 28: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 28: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 28: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 28: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 28: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 28: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSwapStatic 28: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSwapDynamic 28: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 28: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 28: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 28: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 28: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 28: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 28: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 28: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 28: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 28: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 28: [ RUN ] MultiDimArrayTest.conversionToView 28: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 28: [ RUN ] MultiDimArrayTest.conversionToConstView 28: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 28: [ RUN ] MultiDimArrayTest.viewBegin 28: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 28: [ RUN ] MultiDimArrayTest.viewEnd 28: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 28: [ RUN ] MultiDimArrayTest.constViewConstBegin 28: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 28: [ RUN ] MultiDimArrayTest.constViewConstEnd 28: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 28: [----------] 25 tests from MultiDimArrayTest (0 ms total) 28: 28: [----------] 4 tests from MultiDimArrayToMdSpanTest 28: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 28: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 28: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 28: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 28: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 28: 28: [----------] 9 tests from NelderMeadSimplexTest 28: [ RUN ] NelderMeadSimplexTest.BestVertex 28: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 28: [ RUN ] NelderMeadSimplexTest.WorstVertex 28: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 28: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 28: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 28: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 28: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 28: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 28: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 28: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 28: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 28: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 28: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 28: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 28: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 28: [ RUN ] NelderMeadSimplexTest.OrientedLength 28: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 28: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 28: 28: [----------] 2 tests from NelderMead 28: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 28: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 28: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 28: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 28: [----------] 2 tests from NelderMead (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 28: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ResizeWorks 28: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ReserveWorks 28: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/0.CanCopyAssign 28: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/0.CanMoveAssign 28: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/0.CanSwap 28: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 28: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ResizeWorks 28: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ReserveWorks 28: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/1.CanCopyAssign 28: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/1.CanMoveAssign 28: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/1.CanSwap 28: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 28: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ResizeWorks 28: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ReserveWorks 28: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/2.CanCopyAssign 28: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/2.CanMoveAssign 28: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/2.CanSwap 28: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 28: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ResizeWorks 28: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ReserveWorks 28: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/3.CanCopyAssign 28: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/3.CanMoveAssign 28: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/3.CanSwap 28: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 28: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ResizeWorks 28: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ReserveWorks 28: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/4.CanCopyAssign 28: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/4.CanMoveAssign 28: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/4.CanSwap 28: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 28: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ResizeWorks 28: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ReserveWorks 28: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/5.CanCopyAssign 28: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/5.CanMoveAssign 28: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/5.CanSwap 28: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 28: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ResizeWorks 28: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ReserveWorks 28: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/6.CanCopyAssign 28: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/6.CanMoveAssign 28: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/6.CanSwap 28: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 28: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ResizeWorks 28: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ReserveWorks 28: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/7.CanCopyAssign 28: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/7.CanMoveAssign 28: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/7.CanSwap 28: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 28: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ResizeWorks 28: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ReserveWorks 28: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/8.CanCopyAssign 28: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/8.CanMoveAssign 28: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/8.CanSwap 28: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 28: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ResizeWorks 28: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ReserveWorks 28: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/9.CanCopyAssign 28: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/9.CanMoveAssign 28: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/9.CanSwap 28: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 28: 28: [----------] 39 tests from RVecTest 28: [ RUN ] RVecTest.CanBeStoredInVector 28: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 28: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 28: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 28: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 28: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 28: [ RUN ] RVecTest.WorksAsMutable_rvec 28: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 28: [ RUN ] RVecTest.WorksAs_rvec_Array 28: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 28: [ RUN ] RVecTest.ComparesEqual 28: [ OK ] RVecTest.ComparesEqual (0 ms) 28: [ RUN ] RVecTest.ComparesUnequal 28: [ OK ] RVecTest.ComparesUnequal (0 ms) 28: [ RUN ] RVecTest.CanAddRVecToRvec 28: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 28: [ RUN ] RVecTest.CanAddAssignRVecToRvec 28: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 28: [ RUN ] RVecTest.CanSubtractRVecFromRvec 28: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 28: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 28: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 28: [ RUN ] RVecTest.CanDotProductRVecByRvec 28: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 28: [ RUN ] RVecTest.CanCrossProductRVecByRvec 28: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 28: [ RUN ] RVecTest.CanDivideRVecInplace 28: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 28: [ RUN ] RVecTest.CanScaleRVec 28: [ OK ] RVecTest.CanScaleRVec (0 ms) 28: [ RUN ] RVecTest.CanDivideRVec 28: [ OK ] RVecTest.CanDivideRVec (0 ms) 28: [ RUN ] RVecTest.CanDoUnitvFromRVec 28: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 28: [ RUN ] RVecTest.CanSqLengthOfRVec 28: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanLengthOfRVec 28: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanCastToRVec 28: [ OK ] RVecTest.CanCastToRVec (0 ms) 28: [ RUN ] RVecTest.CanCastToDVec 28: [ OK ] RVecTest.CanCastToDVec (0 ms) 28: [ RUN ] RVecTest.CanLeftScalarMultiply 28: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 28: [ RUN ] RVecTest.CanRightScalarMultiply 28: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 28: [ RUN ] RVecTest.CanGetUnitvFromRVec 28: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 28: [ RUN ] RVecTest.CanGetSqLengthOfRVec 28: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanGetLengthOfRVec 28: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanDoCrossProductOfRVec 28: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 28: [ RUN ] RVecTest.CanDoDotProductOfRVec 28: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 28: [ RUN ] RVecTest.CanScaleByVector 28: [ OK ] RVecTest.CanScaleByVector (0 ms) 28: [ RUN ] RVecTest.asIVec 28: [ OK ] RVecTest.asIVec (0 ms) 28: [ RUN ] RVecTest.elementWiseMin 28: [ OK ] RVecTest.elementWiseMin (0 ms) 28: [ RUN ] RVecTest.elementWiseMax 28: [ OK ] RVecTest.elementWiseMax (0 ms) 28: [ RUN ] RVecTest.WorksAs_dvec_Reference 28: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 28: [ RUN ] RVecTest.WorksAs_ivec_Reference 28: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 28: [ RUN ] RVecTest.WorksAs_rvec_Reference 28: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 28: [ RUN ] RVecTest.CopyConstructorWorks 28: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 28: [ RUN ] RVecTest.CopyAssignmentWorks 28: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 28: [ RUN ] RVecTest.MoveConstructorWorks 28: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 28: [ RUN ] RVecTest.MoveAssignmentWorks 28: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 28: [----------] 39 tests from RVecTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 301 tests from 38 test suites ran. (100 ms total) 28: [ PASSED ] 301 tests. 28/81 Test #28: MathUnitTests .................................. Passed 0.21 sec test 29 Start 29: MdrunUtilityUnitTests 29: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests 29: Test timeout computed to be: 30 29: [==========] Running 17 tests from 1 test suite. 29: [----------] Global test environment set-up. 29: [----------] 17 tests from ThreadAffinityTest 29: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 29: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 29: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 29: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 29: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 29: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 29: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 29: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 29: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 29: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 29: NOTE: Affinity setting failed. 29: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms) 29: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 29: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (15 ms) 29: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 29: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (11 ms) 29: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 29: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (7 ms) 29: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 29: NOTE: Affinity setting for 1/2 threads failed. 29: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (8 ms) 29: [----------] 17 tests from ThreadAffinityTest (47 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 17 tests from 1 test suite ran. (47 ms total) 29: [ PASSED ] 17 tests. 29/81 Test #29: MdrunUtilityUnitTests .......................... Passed 0.07 sec test 30 Start 30: MdrunUtilityMpiUnitTests 30: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdrunutility/tests 30: Test timeout computed to be: 30 30: [==========] Running 13 tests from 2 test suites. 30: [----------] Global test environment set-up. 30: [----------] 6 tests from ThreadAffinityMultiRankTest 30: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 30: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (55 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 30: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (99 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 30: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (59 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 30: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (39 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 30: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (83 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 30: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (64 ms) 30: [----------] 6 tests from ThreadAffinityMultiRankTest (404 ms total) 30: 30: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (104 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (87 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (55 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (179 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (67 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (87 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (75 ms) 30: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (659 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 13 tests from 2 test suites ran. (1063 ms total) 30: [ PASSED ] 13 tests. 30/81 Test #30: MdrunUtilityMpiUnitTests ....................... Passed 1.09 sec test 31 Start 31: MDSpanTests 31: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdspan/tests 31: Test timeout computed to be: 30 31: [==========] Running 32 tests from 7 test suites. 31: [----------] Global test environment set-up. 31: [----------] 4 tests from BasicAccessorPolicy 31: [ RUN ] BasicAccessorPolicy.Decay 31: [ OK ] BasicAccessorPolicy.Decay (0 ms) 31: [ RUN ] BasicAccessorPolicy.Access 31: [ OK ] BasicAccessorPolicy.Access (0 ms) 31: [ RUN ] BasicAccessorPolicy.Offset 31: [ OK ] BasicAccessorPolicy.Offset (0 ms) 31: [ RUN ] BasicAccessorPolicy.CopyAccessor 31: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 31: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 31: 31: [----------] 4 tests from ExtentsTest 31: [ RUN ] ExtentsTest.Construction 31: [ OK ] ExtentsTest.Construction (0 ms) 31: [ RUN ] ExtentsTest.PurelyStatic 31: [ OK ] ExtentsTest.PurelyStatic (0 ms) 31: [ RUN ] ExtentsTest.RankNought 31: [ OK ] ExtentsTest.RankNought (0 ms) 31: [ RUN ] ExtentsTest.Assignment 31: [ OK ] ExtentsTest.Assignment (0 ms) 31: [----------] 4 tests from ExtentsTest (0 ms total) 31: 31: [----------] 8 tests from MdSpanExtension 31: [ RUN ] MdSpanExtension.SlicingAllStatic 31: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 31: [ RUN ] MdSpanExtension.SlicingDynamic 31: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 31: [ RUN ] MdSpanExtension.SlicingAllStatic3D 31: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 31: [ RUN ] MdSpanExtension.SlicingEqualsView3D 31: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 31: [ RUN ] MdSpanExtension.additionWorks 31: [ OK ] MdSpanExtension.additionWorks (0 ms) 31: [ RUN ] MdSpanExtension.subtractionWorks 31: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 31: [ RUN ] MdSpanExtension.multiplicationWorks 31: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 31: [ RUN ] MdSpanExtension.divisionWorks 31: [ OK ] MdSpanExtension.divisionWorks (0 ms) 31: [----------] 8 tests from MdSpanExtension (0 ms total) 31: 31: [----------] 3 tests from LayoutTests 31: [ RUN ] LayoutTests.LayoutRightConstruction 31: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 31: [ RUN ] LayoutTests.LayoutRightProperties 31: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 31: [ RUN ] LayoutTests.LayoutRightOperator 31: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 31: [----------] 3 tests from LayoutTests (0 ms total) 31: 31: [----------] 1 test from MdSpanTest 31: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 31: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 31: [----------] 1 test from MdSpanTest (0 ms total) 31: 31: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 31: [ RUN ] MdSpanTest/0.Rank 31: [ OK ] MdSpanTest/0.Rank (0 ms) 31: [ RUN ] MdSpanTest/0.DynamicRank 31: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 31: [ RUN ] MdSpanTest/0.Extents 31: [ OK ] MdSpanTest/0.Extents (0 ms) 31: [ RUN ] MdSpanTest/0.Strides 31: [ OK ] MdSpanTest/0.Strides (0 ms) 31: [ RUN ] MdSpanTest/0.Properties 31: [ OK ] MdSpanTest/0.Properties (0 ms) 31: [ RUN ] MdSpanTest/0.Operator 31: [ OK ] MdSpanTest/0.Operator (0 ms) 31: [----------] 6 tests from MdSpanTest/0 (0 ms total) 31: 31: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 31: [ RUN ] MdSpanTest/1.Rank 31: [ OK ] MdSpanTest/1.Rank (0 ms) 31: [ RUN ] MdSpanTest/1.DynamicRank 31: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 31: [ RUN ] MdSpanTest/1.Extents 31: [ OK ] MdSpanTest/1.Extents (0 ms) 31: [ RUN ] MdSpanTest/1.Strides 31: [ OK ] MdSpanTest/1.Strides (0 ms) 31: [ RUN ] MdSpanTest/1.Properties 31: [ OK ] MdSpanTest/1.Properties (0 ms) 31: [ RUN ] MdSpanTest/1.Operator 31: [ OK ] MdSpanTest/1.Operator (0 ms) 31: [----------] 6 tests from MdSpanTest/1 (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 32 tests from 7 test suites ran. (0 ms total) 31: [ PASSED ] 32 tests. 31/81 Test #31: MDSpanTests .................................... Passed 0.06 sec test 32 Start 32: MdtypesUnitTest 32: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml" 32: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/mdtypes/tests 32: Test timeout computed to be: 30 32: [==========] Running 93 tests from 6 test suites. 32: [----------] Global test environment set-up. 32: [----------] 4 tests from ObservablesReducerTest 32: [ RUN ] ObservablesReducerTest.CanMoveAssign 32: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 32: [ RUN ] ObservablesReducerTest.CanMoveConstruct 32: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 32: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 32: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 32: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 32: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 32: [----------] 4 tests from ObservablesReducerTest (0 ms total) 32: 32: [----------] 2 tests from CheckpointDataTest 32: [ RUN ] CheckpointDataTest.SingleDataTest 32: [ OK ] CheckpointDataTest.SingleDataTest (1 ms) 32: [ RUN ] CheckpointDataTest.MultiDataTest 32: [ OK ] CheckpointDataTest.MultiDataTest (15 ms) 32: [----------] 2 tests from CheckpointDataTest (17 ms total) 32: 32: [----------] 7 tests from ForceBuffers 32: [ RUN ] ForceBuffers.ConstructsUnpinned 32: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 32: [ RUN ] ForceBuffers.ConstructsPinned 32: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 32: [ RUN ] ForceBuffers.ConstructsEmpty 32: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 32: [ RUN ] ForceBuffers.ResizeWorks 32: [ OK ] ForceBuffers.ResizeWorks (0 ms) 32: [ RUN ] ForceBuffers.PaddingWorks 32: [ OK ] ForceBuffers.PaddingWorks (0 ms) 32: [ RUN ] ForceBuffers.CopyWorks 32: [ OK ] ForceBuffers.CopyWorks (0 ms) 32: [ RUN ] ForceBuffers.CopyDoesNotPin 32: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 32: [----------] 7 tests from ForceBuffers (0 ms total) 32: 32: [----------] 5 tests from MultipleTimeStepping 32: [ RUN ] MultipleTimeStepping.ChecksNumLevels 32: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 32: [ RUN ] MultipleTimeStepping.SelectsForceGroups 32: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 32: [ RUN ] MultipleTimeStepping.ChecksStepFactor 32: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 32: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 32: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 32: [ RUN ] MultipleTimeStepping.ChecksIntegrator 32: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 32: [----------] 5 tests from MultipleTimeStepping (0 ms total) 32: 32: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (8 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 32: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (11 ms total) 32: 32: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 32: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 93 tests from 6 test suites ran. (28 ms total) 32: [ PASSED ] 93 tests. 32/81 Test #32: MdtypesUnitTest ................................ Passed 0.09 sec test 33 Start 33: OnlineHelpUnitTests 33: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/onlinehelp/tests 33: Test timeout computed to be: 30 33: [==========] Running 22 tests from 4 test suites. 33: [----------] Global test environment set-up. 33: [----------] 6 tests from TextTableFormatterTest 33: [ RUN ] TextTableFormatterTest.HandlesBasicCase 33: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 33: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 33: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 33: [ RUN ] TextTableFormatterTest.HandlesIndentation 33: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 33: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 33: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 33: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 33: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 33: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 33: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 33: [----------] 6 tests from TextTableFormatterTest (0 ms total) 33: 33: [----------] 3 tests from HelpManagerTest 33: [ RUN ] HelpManagerTest.HandlesRootTopic 33: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 33: [ RUN ] HelpManagerTest.HandlesSubTopics 33: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 33: [ RUN ] HelpManagerTest.HandlesInvalidTopics 33: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 33: [----------] 3 tests from HelpManagerTest (0 ms total) 33: 33: [----------] 2 tests from HelpTopicFormattingTest 33: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 33: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 33: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 33: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 33: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 33: 33: [----------] 11 tests from HelpWriterContextTest 33: [ RUN ] HelpWriterContextTest.FormatsParagraphs 33: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 33: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 33: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 33: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsLiteralText 33: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 33: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 33: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsBulletList 33: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 33: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 33: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsGridTable 33: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsTitles 33: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 33: [----------] 11 tests from HelpWriterContextTest (1 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 22 tests from 4 test suites ran. (2 ms total) 33: [ PASSED ] 22 tests. 33/81 Test #33: OnlineHelpUnitTests ............................ Passed 0.06 sec test 34 Start 34: OptionsUnitTests 34: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/options/tests 34: Test timeout computed to be: 30 34: [==========] Running 111 tests from 18 test suites. 34: [----------] Global test environment set-up. 34: [----------] 5 tests from AbstractOptionStorageTest 34: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 34: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 34: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 34: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 34: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 34: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 34: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 34: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 34: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 34: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 34: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 34: 34: [----------] 10 tests from FileNameOptionTest 34: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 34: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 34: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 34: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 34: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 34: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 34: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 34: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 34: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 34: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 34: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 34: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 34: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 34: [----------] 10 tests from FileNameOptionTest (0 ms total) 34: 34: [----------] 15 tests from FileNameOptionManagerTest 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 34: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 34: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 34: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 34: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 34: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 34: [----------] 15 tests from FileNameOptionManagerTest (0 ms total) 34: 34: [----------] 1 test from OptionsTest 34: [ RUN ] OptionsTest.FailsOnNonsafeStorage 34: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 34: [----------] 1 test from OptionsTest (0 ms total) 34: 34: [----------] 9 tests from OptionsAssignerTest 34: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 34: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 34: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 34: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 34: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesMissingValue 34: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesExtraValue 34: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesGroups 34: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesSections 34: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 34: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 34: [----------] 9 tests from OptionsAssignerTest (0 ms total) 34: 34: [----------] 4 tests from OptionsAssignerBooleanTest 34: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 34: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 34: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 34: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 34: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 34: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 34: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 34: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 34: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 34: 34: [----------] 13 tests from OptionsAssignerIntegerTest 34: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 34: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 34: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 34: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 34: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 34: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 34: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 34: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 34: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 34: 34: [----------] 5 tests from OptionsAssignerDoubleTest 34: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 34: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 34: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 34: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 34: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 34: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 34: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 34: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 34: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 34: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 34: 34: [----------] 9 tests from OptionsAssignerStringTest 34: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 34: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 34: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 34: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 34: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 34: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 34: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 34: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 34: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 34: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 34: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 34: 34: [----------] 6 tests from OptionsAssignerEnumTest 34: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 34: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 34: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 34: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 34: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 34: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 34: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 34: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 34: 34: [----------] 8 tests from RepeatingOptionSectionTest 34: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 34: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 34: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 34: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 34: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 34: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 34: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 34: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 34: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 34: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 34: 34: [----------] 1 test from TimeUnitManagerTest 34: [ RUN ] TimeUnitManagerTest.BasicOperations 34: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 34: [----------] 1 test from TimeUnitManagerTest (0 ms total) 34: 34: [----------] 4 tests from TimeUnitBehaviorTest 34: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 34: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 34: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 34: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 34: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 34: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 34: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 34: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 34: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 34: 34: [----------] 2 tests from TreeValueSupportAssignTest 34: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 34: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 34: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 34: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 34: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 34: 34: [----------] 1 test from TreeValueSupportAssignErrorTest 34: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 34: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 34: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 34: 34: [----------] 5 tests from TreeValueSupportCheckTest 34: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 34: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 34: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 34: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 34: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 34: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 34: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 34: 34: [----------] 6 tests from TreeValueSupportAdjustTest 34: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 34: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 34: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 34: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 34: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 34: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 34: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 34: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 34: 34: [----------] 7 tests from TreeValueSupportTest 34: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 34: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 34: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsInt64Option 34: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsStringOption 34: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsFloatOption 34: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 34: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsEnumOption 34: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 34: [----------] 7 tests from TreeValueSupportTest (1 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 111 tests from 18 test suites ran. (5 ms total) 34: [ PASSED ] 111 tests. 34/81 Test #34: OptionsUnitTests ............................... Passed 0.09 sec test 35 Start 35: PbcutilUnitTest 35: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 35: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pbcutil/tests 35: Test timeout computed to be: 30 35: [==========] Running 33 tests from 5 test suites. 35: [----------] Global test environment set-up. 35: [----------] 1 test from ShiftTest 35: [ RUN ] ShiftTest.CoordinateShiftWorks 35: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 35: [----------] 1 test from ShiftTest (0 ms total) 35: 35: [----------] 2 tests from MShift 35: [ RUN ] MShift.shiftsAndUnshifts 35: [ OK ] MShift.shiftsAndUnshifts (0 ms) 35: [ RUN ] MShift.shiftsAndUnshiftsSelf 35: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 35: [----------] 2 tests from MShift (0 ms total) 35: 35: [----------] 1 test from PbcTest 35: [ RUN ] PbcTest.CalcShiftsWorks 35: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 35: [----------] 1 test from PbcTest (0 ms total) 35: 35: [----------] 2 tests from PbcEnumsTest 35: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 35: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 35: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 35: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 35: [----------] 2 tests from PbcEnumsTest (0 ms total) 35: 35: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (8 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 35: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (15 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 33 tests from 5 test suites ran. (16 ms total) 35: [ PASSED ] 33 tests. 35/81 Test #35: PbcutilUnitTest ................................ Passed 0.08 sec test 36 Start 36: RandomUnitTests 36: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/random/tests 36: Test timeout computed to be: 30 36: [==========] Running 44 tests from 10 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from ExponentialDistributionTest 36: [ RUN ] ExponentialDistributionTest.Output 36: [ OK ] ExponentialDistributionTest.Output (0 ms) 36: [ RUN ] ExponentialDistributionTest.Logical 36: [ OK ] ExponentialDistributionTest.Logical (0 ms) 36: [ RUN ] ExponentialDistributionTest.Reset 36: [ OK ] ExponentialDistributionTest.Reset (0 ms) 36: [ RUN ] ExponentialDistributionTest.AltParam 36: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 36: 36: [----------] 4 tests from GammaDistributionTest 36: [ RUN ] GammaDistributionTest.Output 36: [ OK ] GammaDistributionTest.Output (0 ms) 36: [ RUN ] GammaDistributionTest.Logical 36: [ OK ] GammaDistributionTest.Logical (0 ms) 36: [ RUN ] GammaDistributionTest.Reset 36: [ OK ] GammaDistributionTest.Reset (0 ms) 36: [ RUN ] GammaDistributionTest.AltParam 36: [ OK ] GammaDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from GammaDistributionTest (0 ms total) 36: 36: [----------] 4 tests from NormalDistributionTest 36: [ RUN ] NormalDistributionTest.Output 36: [ OK ] NormalDistributionTest.Output (0 ms) 36: [ RUN ] NormalDistributionTest.Logical 36: [ OK ] NormalDistributionTest.Logical (0 ms) 36: [ RUN ] NormalDistributionTest.Reset 36: [ OK ] NormalDistributionTest.Reset (0 ms) 36: [ RUN ] NormalDistributionTest.AltParam 36: [ OK ] NormalDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from NormalDistributionTest (0 ms total) 36: 36: [----------] 1 test from SeedTest 36: [ RUN ] SeedTest.makeRandomSeed 36: [ OK ] SeedTest.makeRandomSeed (0 ms) 36: [----------] 1 test from SeedTest (0 ms total) 36: 36: [----------] 6 tests from TabulatedNormalDistributionTest 36: [ RUN ] TabulatedNormalDistributionTest.Output14 36: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.Output16 36: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 36: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.Logical 36: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.Reset 36: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.AltParam 36: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 36: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 36: 36: [----------] 1 test from TabulatedNormalDistributionTableTest 36: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 36: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (1 ms) 36: [----------] 1 test from TabulatedNormalDistributionTableTest (1 ms total) 36: 36: [----------] 6 tests from ThreeFry2x64Test 36: [ RUN ] ThreeFry2x64Test.Logical 36: [ OK ] ThreeFry2x64Test.Logical (0 ms) 36: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 36: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 36: [ RUN ] ThreeFry2x64Test.Reseed 36: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 36: [ RUN ] ThreeFry2x64Test.Discard 36: [ OK ] ThreeFry2x64Test.Discard (0 ms) 36: [ RUN ] ThreeFry2x64Test.InvalidCounter 36: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 36: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 36: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 36: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 36: 36: [----------] 4 tests from UniformIntDistributionTest 36: [ RUN ] UniformIntDistributionTest.Output 36: [ OK ] UniformIntDistributionTest.Output (0 ms) 36: [ RUN ] UniformIntDistributionTest.Logical 36: [ OK ] UniformIntDistributionTest.Logical (0 ms) 36: [ RUN ] UniformIntDistributionTest.Reset 36: [ OK ] UniformIntDistributionTest.Reset (0 ms) 36: [ RUN ] UniformIntDistributionTest.AltParam 36: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 36: 36: [----------] 5 tests from UniformRealDistributionTest 36: [ RUN ] UniformRealDistributionTest.GenerateCanonical 36: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 36: [ RUN ] UniformRealDistributionTest.Output 36: [ OK ] UniformRealDistributionTest.Output (0 ms) 36: [ RUN ] UniformRealDistributionTest.Logical 36: [ OK ] UniformRealDistributionTest.Logical (0 ms) 36: [ RUN ] UniformRealDistributionTest.Reset 36: [ OK ] UniformRealDistributionTest.Reset (0 ms) 36: [ RUN ] UniformRealDistributionTest.AltParam 36: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 36: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 36: 36: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 36: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 44 tests from 10 test suites ran. (4 ms total) 36: [ PASSED ] 44 tests. 36/81 Test #36: RandomUnitTests ................................ Passed 0.06 sec test 37 Start 37: RestraintTests 37: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/RestraintTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/restraint/tests 37: Test timeout computed to be: 30 37: [==========] Running 1 test from 1 test suite. 37: [----------] Global test environment set-up. 37: [----------] 1 test from RestraintManager 37: [ RUN ] RestraintManager.restraintList 37: [ OK ] RestraintManager.restraintList (0 ms) 37: [----------] 1 test from RestraintManager (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 1 test from 1 test suite ran. (0 ms total) 37: [ PASSED ] 1 test. 37/81 Test #37: RestraintTests ................................. Passed 0.02 sec test 38 Start 38: TableUnitTests 38: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tables/tests 38: Test timeout computed to be: 30 38: [==========] Running 20 tests from 2 test suites. 38: [----------] Global test environment set-up. 38: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 38: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 38: [ OK ] SplineTableTest/0.HandlesIncorrectInput (2 ms) 38: [ RUN ] SplineTableTest/0.Sinc 38: [ OK ] SplineTableTest/0.Sinc (0 ms) 38: [ RUN ] SplineTableTest/0.LJ12 38: [ OK ] SplineTableTest/0.LJ12 (24 ms) 38: [ RUN ] SplineTableTest/0.PmeCorrection 38: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 38: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 38: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 38: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 38: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 38: [ RUN ] SplineTableTest/0.TwoFunctions 38: [ OK ] SplineTableTest/0.TwoFunctions (48 ms) 38: [ RUN ] SplineTableTest/0.ThreeFunctions 38: [ OK ] SplineTableTest/0.ThreeFunctions (53 ms) 38: [ RUN ] SplineTableTest/0.Simd 38: [ OK ] SplineTableTest/0.Simd (7 ms) 38: [ RUN ] SplineTableTest/0.SimdTwoFunctions 38: [ OK ] SplineTableTest/0.SimdTwoFunctions (35 ms) 38: [----------] 10 tests from SplineTableTest/0 (175 ms total) 38: 38: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 38: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 38: [ OK ] SplineTableTest/1.HandlesIncorrectInput (1 ms) 38: [ RUN ] SplineTableTest/1.Sinc 38: [ OK ] SplineTableTest/1.Sinc (1 ms) 38: [ RUN ] SplineTableTest/1.LJ12 38: [ OK ] SplineTableTest/1.LJ12 (97 ms) 38: [ RUN ] SplineTableTest/1.PmeCorrection 38: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 38: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 38: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 38: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 38: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 38: [ RUN ] SplineTableTest/1.TwoFunctions 38: [ OK ] SplineTableTest/1.TwoFunctions (233 ms) 38: [ RUN ] SplineTableTest/1.ThreeFunctions 38: [ OK ] SplineTableTest/1.ThreeFunctions (237 ms) 38: [ RUN ] SplineTableTest/1.Simd 38: [ OK ] SplineTableTest/1.Simd (45 ms) 38: [ RUN ] SplineTableTest/1.SimdTwoFunctions 38: [ OK ] SplineTableTest/1.SimdTwoFunctions (186 ms) 38: [----------] 10 tests from SplineTableTest/1 (807 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 20 tests from 2 test suites ran. (983 ms total) 38: [ PASSED ] 20 tests. 38/81 Test #38: TableUnitTests ................................. Passed 1.02 sec test 39 Start 39: TaskAssignmentUnitTests 39: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/taskassignment/tests 39: Test timeout computed to be: 30 39: [==========] Running 3 tests from 2 test suites. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 39: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 39: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 39: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 39: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 39: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 39: 39: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 39: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 39: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 39: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 3 tests from 2 test suites ran. (0 ms total) 39: [ PASSED ] 3 tests. 39/81 Test #39: TaskAssignmentUnitTests ........................ Passed 0.03 sec test 40 Start 40: GmxTimingTests 40: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/GmxTimingTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/timing/tests 40: Test timeout computed to be: 30 40: [==========] Running 6 tests from 1 test suite. 40: [----------] Global test environment set-up. 40: [----------] 6 tests from TimingTest 40: [ RUN ] TimingTest.ElementCountingWorks 40: [ OK ] TimingTest.ElementCountingWorks (0 ms) 40: [ RUN ] TimingTest.ElementNoCountingWorks 40: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 40: [ RUN ] TimingTest.SubElementCountingWorks 40: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 40: [ RUN ] TimingTest.SubElementNoCountingWorks 40: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 40: [ RUN ] TimingTest.RunWallCycle 40: [ OK ] TimingTest.RunWallCycle (1 ms) 40: [ RUN ] TimingTest.RunWallCycleSub 40: [ OK ] TimingTest.RunWallCycleSub (0 ms) 40: [----------] 6 tests from TimingTest (1 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 6 tests from 1 test suite ran. (1 ms total) 40: [ PASSED ] 6 tests. 40/81 Test #40: GmxTimingTests ................................. Passed 0.03 sec test 41 Start 41: TopologyTest 41: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/TopologyTest.xml" 41: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/topology/tests 41: Test timeout computed to be: 30 41: [==========] Running 40 tests from 7 test suites. 41: [----------] Global test environment set-up. 41: [----------] 3 tests from ExclusionBlockTest 41: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 41: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 41: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 41: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 41: [ RUN ] ExclusionBlockTest.MergeExclusions 41: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 41: [----------] 3 tests from ExclusionBlockTest (0 ms total) 41: 41: [----------] 6 tests from InteractionListTest 41: [ RUN ] InteractionListTest.EmptyWorks 41: [ OK ] InteractionListTest.EmptyWorks (0 ms) 41: [ RUN ] InteractionListTest.CanAddInteractionArray 41: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 41: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 41: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 41: [ RUN ] InteractionListTest.CanAddInteractionPointer 41: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 41: [ RUN ] InteractionListTest.CanAddListToOtherList 41: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 41: [ RUN ] InteractionListTest.ClearingWorks 41: [ OK ] InteractionListTest.ClearingWorks (0 ms) 41: [----------] 6 tests from InteractionListTest (0 ms total) 41: 41: [----------] 5 tests from MtopTest 41: [ RUN ] MtopTest.RangeBasedLoop 41: [ OK ] MtopTest.RangeBasedLoop (0 ms) 41: [ RUN ] MtopTest.Operators 41: [ OK ] MtopTest.Operators (0 ms) 41: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 41: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 41: [ RUN ] MtopTest.AtomHasPerturbedChargeIn14Interaction 41: [ OK ] MtopTest.AtomHasPerturbedChargeIn14Interaction (0 ms) 41: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 41: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 41: [----------] 5 tests from MtopTest (0 ms total) 41: 41: [----------] 2 tests from IListRangeTest 41: [ RUN ] IListRangeTest.RangeBasedLoopWorks 41: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 41: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 41: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 41: [----------] 2 tests from IListRangeTest (0 ms total) 41: 41: [----------] 13 tests from StringTableTest 41: [ RUN ] StringTableTest.AddSingleEntry 41: [ OK ] StringTableTest.AddSingleEntry (0 ms) 41: [ RUN ] StringTableTest.CanAccessWithAt 41: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 41: [ RUN ] StringTableTest.CanAccessWithBracket 41: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 41: [ RUN ] StringTableTest.ThrowsOutOfRange 41: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 41: [ RUN ] StringTableTest.StringCompareIsCorrect 41: [ OK ] StringTableTest.StringCompareIsCorrect (2 ms) 41: [ RUN ] StringTableTest.AddTwoDistinctEntries 41: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 41: [ RUN ] StringTableTest.TryToAddDuplicates 41: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 41: [ RUN ] StringTableTest.AddLargeNumberOfEntries 41: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 41: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 41: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 41: [ RUN ] StringTableTest.CanWriteToBuffer 41: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 41: [ RUN ] StringTableTest.Roundtrip 41: [ OK ] StringTableTest.Roundtrip (0 ms) 41: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 41: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 41: [ RUN ] StringTableTest.CanCopyToLegacyTable 41: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 41: [----------] 13 tests from StringTableTest (3 ms total) 41: 41: [----------] 6 tests from LegacySymtabTest 41: [ RUN ] LegacySymtabTest.EmptyOnOpen 41: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 41: [ RUN ] LegacySymtabTest.AddSingleEntry 41: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 41: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 41: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 41: [ RUN ] LegacySymtabTest.TryToAddDuplicates 41: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 41: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 41: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 41: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 41: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 41: [----------] 6 tests from LegacySymtabTest (0 ms total) 41: 41: [----------] 5 tests from TopSortTest 41: [ RUN ] TopSortTest.WorksOnEmptyIdef 41: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 41: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 41: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 41: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 41: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 41: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 41: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 41: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 41: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 41: [----------] 5 tests from TopSortTest (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 40 tests from 7 test suites ran. (4 ms total) 41: [ PASSED ] 40 tests. 41/81 Test #41: TopologyTest ................................... Passed 0.03 sec test 42 Start 42: PullTest 42: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/PullTest.xml" 42: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/pulling/tests 42: Test timeout computed to be: 30 42: [==========] Running 8 tests from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 8 tests from PullTest 42: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 42: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 42: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 42: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 42: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 42: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 42: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 42: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 42: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 42: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 42: [ RUN ] PullTest.TransformationCoordSimple 42: [ OK ] PullTest.TransformationCoordSimple (0 ms) 42: [ RUN ] PullTest.TransformationCoordAdvanced 42: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 42: [ RUN ] PullTest.TransformationCoordDummyExpression 42: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 42: [----------] 8 tests from PullTest (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 8 tests from 1 test suite ran. (1 ms total) 42: [ PASSED ] 8 tests. 42/81 Test #42: PullTest ....................................... Passed 0.03 sec test 43 Start 43: SimdUnitTests 43: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/simd/tests 43: Test timeout computed to be: 30 43: [==========] Running 247 tests from 19 test suites. 43: [----------] Global test environment set-up. 43: [----------] 6 tests from SimdBootstrapTest 43: [ RUN ] SimdBootstrapTest.loadStore 43: [ OK ] SimdBootstrapTest.loadStore (0 ms) 43: [ RUN ] SimdBootstrapTest.loadU 43: [ OK ] SimdBootstrapTest.loadU (0 ms) 43: [ RUN ] SimdBootstrapTest.storeU 43: [ OK ] SimdBootstrapTest.storeU (0 ms) 43: [ RUN ] SimdBootstrapTest.loadStoreI 43: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 43: [ RUN ] SimdBootstrapTest.loadUI 43: [ OK ] SimdBootstrapTest.loadUI (0 ms) 43: [ RUN ] SimdBootstrapTest.storeUI 43: [ OK ] SimdBootstrapTest.storeUI (0 ms) 43: [----------] 6 tests from SimdBootstrapTest (0 ms total) 43: 43: [----------] 41 tests from SimdScalarTest 43: [ RUN ] SimdScalarTest.load 43: [ OK ] SimdScalarTest.load (0 ms) 43: [ RUN ] SimdScalarTest.loadU 43: [ OK ] SimdScalarTest.loadU (0 ms) 43: [ RUN ] SimdScalarTest.store 43: [ OK ] SimdScalarTest.store (0 ms) 43: [ RUN ] SimdScalarTest.storeU 43: [ OK ] SimdScalarTest.storeU (0 ms) 43: [ RUN ] SimdScalarTest.setZero 43: [ OK ] SimdScalarTest.setZero (0 ms) 43: [ RUN ] SimdScalarTest.andNot 43: [ OK ] SimdScalarTest.andNot (0 ms) 43: [ RUN ] SimdScalarTest.fma 43: [ OK ] SimdScalarTest.fma (0 ms) 43: [ RUN ] SimdScalarTest.fms 43: [ OK ] SimdScalarTest.fms (0 ms) 43: [ RUN ] SimdScalarTest.fnma 43: [ OK ] SimdScalarTest.fnma (0 ms) 43: [ RUN ] SimdScalarTest.fnms 43: [ OK ] SimdScalarTest.fnms (0 ms) 43: [ RUN ] SimdScalarTest.maskAdd 43: [ OK ] SimdScalarTest.maskAdd (0 ms) 43: [ RUN ] SimdScalarTest.maskzMul 43: [ OK ] SimdScalarTest.maskzMul (0 ms) 43: [ RUN ] SimdScalarTest.maskzFma 43: [ OK ] SimdScalarTest.maskzFma (0 ms) 43: [ RUN ] SimdScalarTest.abs 43: [ OK ] SimdScalarTest.abs (0 ms) 43: [ RUN ] SimdScalarTest.max 43: [ OK ] SimdScalarTest.max (0 ms) 43: [ RUN ] SimdScalarTest.min 43: [ OK ] SimdScalarTest.min (0 ms) 43: [ RUN ] SimdScalarTest.round 43: [ OK ] SimdScalarTest.round (0 ms) 43: [ RUN ] SimdScalarTest.trunc 43: [ OK ] SimdScalarTest.trunc (0 ms) 43: [ RUN ] SimdScalarTest.reduce 43: [ OK ] SimdScalarTest.reduce (0 ms) 43: [ RUN ] SimdScalarTest.testBits 43: [ OK ] SimdScalarTest.testBits (0 ms) 43: [ RUN ] SimdScalarTest.anyTrue 43: [ OK ] SimdScalarTest.anyTrue (0 ms) 43: [ RUN ] SimdScalarTest.selectByMask 43: [ OK ] SimdScalarTest.selectByMask (0 ms) 43: [ RUN ] SimdScalarTest.selectByNotMask 43: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 43: [ RUN ] SimdScalarTest.blend 43: [ OK ] SimdScalarTest.blend (0 ms) 43: [ RUN ] SimdScalarTest.cvtR2I 43: [ OK ] SimdScalarTest.cvtR2I (0 ms) 43: [ RUN ] SimdScalarTest.cvttR2I 43: [ OK ] SimdScalarTest.cvttR2I (0 ms) 43: [ RUN ] SimdScalarTest.cvtI2R 43: [ OK ] SimdScalarTest.cvtI2R (0 ms) 43: [ RUN ] SimdScalarTest.cvtF2D 43: [ OK ] SimdScalarTest.cvtF2D (0 ms) 43: [ RUN ] SimdScalarTest.cvtD2D 43: [ OK ] SimdScalarTest.cvtD2D (0 ms) 43: [ RUN ] SimdScalarTest.loadI 43: [ OK ] SimdScalarTest.loadI (0 ms) 43: [ RUN ] SimdScalarTest.loadUI 43: [ OK ] SimdScalarTest.loadUI (0 ms) 43: [ RUN ] SimdScalarTest.storeI 43: [ OK ] SimdScalarTest.storeI (0 ms) 43: [ RUN ] SimdScalarTest.storeUI 43: [ OK ] SimdScalarTest.storeUI (0 ms) 43: [ RUN ] SimdScalarTest.andNotI 43: [ OK ] SimdScalarTest.andNotI (0 ms) 43: [ RUN ] SimdScalarTest.testBitsI 43: [ OK ] SimdScalarTest.testBitsI (0 ms) 43: [ RUN ] SimdScalarTest.selectByMaskI 43: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 43: [ RUN ] SimdScalarTest.selectByNotMaskI 43: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 43: [ RUN ] SimdScalarTest.blendI 43: [ OK ] SimdScalarTest.blendI (0 ms) 43: [ RUN ] SimdScalarTest.cvtB2IB 43: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 43: [ RUN ] SimdScalarTest.cvtIB2B 43: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 43: [ RUN ] SimdScalarTest.expandScalarsToTriplets 43: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 43: [----------] 41 tests from SimdScalarTest (0 ms total) 43: 43: [----------] 8 tests from SimdScalarUtilTest 43: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 43: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 43: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 43: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 43: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 43: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 43: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 43: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 43: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 43: 43: [----------] 37 tests from SimdScalarMathTest 43: [ RUN ] SimdScalarMathTest.copysign 43: [ OK ] SimdScalarMathTest.copysign (0 ms) 43: [ RUN ] SimdScalarMathTest.invsqrtPair 43: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 43: [ RUN ] SimdScalarMathTest.inv 43: [ OK ] SimdScalarMathTest.inv (0 ms) 43: [ RUN ] SimdScalarMathTest.maskzInvsqrt 43: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 43: [ RUN ] SimdScalarMathTest.log 43: [ OK ] SimdScalarMathTest.log (0 ms) 43: [ RUN ] SimdScalarMathTest.exp2 43: [ OK ] SimdScalarMathTest.exp2 (0 ms) 43: [ RUN ] SimdScalarMathTest.exp 43: [ OK ] SimdScalarMathTest.exp (0 ms) 43: [ RUN ] SimdScalarMathTest.erf 43: [ OK ] SimdScalarMathTest.erf (0 ms) 43: [ RUN ] SimdScalarMathTest.erfc 43: [ OK ] SimdScalarMathTest.erfc (0 ms) 43: [ RUN ] SimdScalarMathTest.sincos 43: [ OK ] SimdScalarMathTest.sincos (0 ms) 43: [ RUN ] SimdScalarMathTest.sin 43: [ OK ] SimdScalarMathTest.sin (0 ms) 43: [ RUN ] SimdScalarMathTest.cos 43: [ OK ] SimdScalarMathTest.cos (0 ms) 43: [ RUN ] SimdScalarMathTest.tan 43: [ OK ] SimdScalarMathTest.tan (0 ms) 43: [ RUN ] SimdScalarMathTest.asin 43: [ OK ] SimdScalarMathTest.asin (0 ms) 43: [ RUN ] SimdScalarMathTest.acos 43: [ OK ] SimdScalarMathTest.acos (0 ms) 43: [ RUN ] SimdScalarMathTest.atan 43: [ OK ] SimdScalarMathTest.atan (0 ms) 43: [ RUN ] SimdScalarMathTest.atan2 43: [ OK ] SimdScalarMathTest.atan2 (0 ms) 43: [ RUN ] SimdScalarMathTest.pmeForceCorrection 43: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 43: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 43: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 43: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 43: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.invSingleAccuracy 43: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 43: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.logSingleAccuracy 43: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 43: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.expSingleAccuracy 43: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 43: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 43: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 43: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 43: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 43: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 43: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 43: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 43: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 43: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 43: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 43: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 43: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 43: [----------] 37 tests from SimdScalarMathTest (0 ms total) 43: 43: [----------] 1 test from SimdTest 43: [ RUN ] SimdTest.GmxAligned 43: [ OK ] SimdTest.GmxAligned (0 ms) 43: [----------] 1 test from SimdTest (0 ms total) 43: 43: [----------] 42 tests from SimdFloatingpointTest 43: [ RUN ] SimdFloatingpointTest.setZero 43: [ OK ] SimdFloatingpointTest.setZero (0 ms) 43: [ RUN ] SimdFloatingpointTest.set 43: [ OK ] SimdFloatingpointTest.set (0 ms) 43: [ RUN ] SimdFloatingpointTest.add 43: [ OK ] SimdFloatingpointTest.add (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskAdd 43: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 43: [ RUN ] SimdFloatingpointTest.sub 43: [ OK ] SimdFloatingpointTest.sub (0 ms) 43: [ RUN ] SimdFloatingpointTest.mul 43: [ OK ] SimdFloatingpointTest.mul (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzMul 43: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 43: [ RUN ] SimdFloatingpointTest.fma 43: [ OK ] SimdFloatingpointTest.fma (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzFma 43: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 43: [ RUN ] SimdFloatingpointTest.fms 43: [ OK ] SimdFloatingpointTest.fms (0 ms) 43: [ RUN ] SimdFloatingpointTest.fnma 43: [ OK ] SimdFloatingpointTest.fnma (0 ms) 43: [ RUN ] SimdFloatingpointTest.fnms 43: [ OK ] SimdFloatingpointTest.fnms (0 ms) 43: [ RUN ] SimdFloatingpointTest.abs 43: [ OK ] SimdFloatingpointTest.abs (0 ms) 43: [ RUN ] SimdFloatingpointTest.neg 43: [ OK ] SimdFloatingpointTest.neg (0 ms) 43: [ RUN ] SimdFloatingpointTest.and 43: [ OK ] SimdFloatingpointTest.and (0 ms) 43: [ RUN ] SimdFloatingpointTest.or 43: [ OK ] SimdFloatingpointTest.or (0 ms) 43: [ RUN ] SimdFloatingpointTest.xor 43: [ OK ] SimdFloatingpointTest.xor (0 ms) 43: [ RUN ] SimdFloatingpointTest.andNot 43: [ OK ] SimdFloatingpointTest.andNot (0 ms) 43: [ RUN ] SimdFloatingpointTest.max 43: [ OK ] SimdFloatingpointTest.max (0 ms) 43: [ RUN ] SimdFloatingpointTest.min 43: [ OK ] SimdFloatingpointTest.min (0 ms) 43: [ RUN ] SimdFloatingpointTest.round 43: [ OK ] SimdFloatingpointTest.round (0 ms) 43: [ RUN ] SimdFloatingpointTest.roundMode 43: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 43: [ RUN ] SimdFloatingpointTest.trunc 43: [ OK ] SimdFloatingpointTest.trunc (0 ms) 43: [ RUN ] SimdFloatingpointTest.frexp 43: [ OK ] SimdFloatingpointTest.frexp (0 ms) 43: [ RUN ] SimdFloatingpointTest.ldexp 43: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 43: [ RUN ] SimdFloatingpointTest.rsqrt 43: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzRsqrt 43: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 43: [ RUN ] SimdFloatingpointTest.rcp 43: [ OK ] SimdFloatingpointTest.rcp (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzRcp 43: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 43: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 43: [ RUN ] SimdFloatingpointTest.selectByNotMask 43: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpNe 43: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpLe 43: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpLt 43: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 43: [ RUN ] SimdFloatingpointTest.testBits 43: [ OK ] SimdFloatingpointTest.testBits (0 ms) 43: [ RUN ] SimdFloatingpointTest.andB 43: [ OK ] SimdFloatingpointTest.andB (0 ms) 43: [ RUN ] SimdFloatingpointTest.orB 43: [ OK ] SimdFloatingpointTest.orB (0 ms) 43: [ RUN ] SimdFloatingpointTest.anyTrueB 43: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 43: [ RUN ] SimdFloatingpointTest.blend 43: [ OK ] SimdFloatingpointTest.blend (0 ms) 43: [ RUN ] SimdFloatingpointTest.reduce 43: [ OK ] SimdFloatingpointTest.reduce (0 ms) 43: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 43: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 43: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 43: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 43: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 43: 43: [----------] 13 tests from SimdFloatingpointUtilTest 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 43: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 43: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 43: [----------] 13 tests from SimdFloatingpointUtilTest (0 ms total) 43: 43: [----------] 23 tests from SimdIntegerTest 43: [ RUN ] SimdIntegerTest.setZero 43: [ OK ] SimdIntegerTest.setZero (0 ms) 43: [ RUN ] SimdIntegerTest.set 43: [ OK ] SimdIntegerTest.set (0 ms) 43: [ RUN ] SimdIntegerTest.add 43: [ OK ] SimdIntegerTest.add (0 ms) 43: [ RUN ] SimdIntegerTest.sub 43: [ OK ] SimdIntegerTest.sub (0 ms) 43: [ RUN ] SimdIntegerTest.mul 43: [ OK ] SimdIntegerTest.mul (0 ms) 43: [ RUN ] SimdIntegerTest.and 43: [ OK ] SimdIntegerTest.and (0 ms) 43: [ RUN ] SimdIntegerTest.andNot 43: [ OK ] SimdIntegerTest.andNot (0 ms) 43: [ RUN ] SimdIntegerTest.or 43: [ OK ] SimdIntegerTest.or (0 ms) 43: [ RUN ] SimdIntegerTest.xor 43: [ OK ] SimdIntegerTest.xor (0 ms) 43: [ RUN ] SimdIntegerTest.extract 43: [ OK ] SimdIntegerTest.extract (0 ms) 43: [ RUN ] SimdIntegerTest.cvtR2I 43: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 43: [ RUN ] SimdIntegerTest.cvttR2I 43: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 43: [ RUN ] SimdIntegerTest.cvtI2R 43: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 43: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 43: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 43: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 43: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 43: [ RUN ] SimdIntegerTest.cmpLt 43: [ OK ] SimdIntegerTest.cmpLt (0 ms) 43: [ RUN ] SimdIntegerTest.testBits 43: [ OK ] SimdIntegerTest.testBits (0 ms) 43: [ RUN ] SimdIntegerTest.andB 43: [ OK ] SimdIntegerTest.andB (0 ms) 43: [ RUN ] SimdIntegerTest.orB 43: [ OK ] SimdIntegerTest.orB (0 ms) 43: [ RUN ] SimdIntegerTest.anyTrue 43: [ OK ] SimdIntegerTest.anyTrue (0 ms) 43: [ RUN ] SimdIntegerTest.blend 43: [ OK ] SimdIntegerTest.blend (0 ms) 43: [ RUN ] SimdIntegerTest.cvtB2IB 43: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 43: [ RUN ] SimdIntegerTest.cvtIB2B 43: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 43: [----------] 23 tests from SimdIntegerTest (0 ms total) 43: 43: [----------] 56 tests from SimdMathTest 43: [ RUN ] SimdMathTest.generateTestPointsDouble 43: [ OK ] SimdMathTest.generateTestPointsDouble (11 ms) 43: [ RUN ] SimdMathTest.copysign 43: [ OK ] SimdMathTest.copysign (0 ms) 43: [ RUN ] SimdMathTest.invsqrt 43: [ OK ] SimdMathTest.invsqrt (0 ms) 43: [ RUN ] SimdMathTest.maskzInvsqrt 43: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 43: [ RUN ] SimdMathTest.invsqrtPair 43: [ OK ] SimdMathTest.invsqrtPair (1 ms) 43: [ RUN ] SimdMathTest.sqrt 43: [ OK ] SimdMathTest.sqrt (2 ms) 43: [ RUN ] SimdMathTest.sqrtUnsafe 43: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 43: [ RUN ] SimdMathTest.inv 43: [ OK ] SimdMathTest.inv (2 ms) 43: [ RUN ] SimdMathTest.maskzInv 43: [ OK ] SimdMathTest.maskzInv (0 ms) 43: [ RUN ] SimdMathTest.cbrt 43: [ OK ] SimdMathTest.cbrt (1 ms) 43: [ RUN ] SimdMathTest.invcbrt 43: [ OK ] SimdMathTest.invcbrt (2 ms) 43: [ RUN ] SimdMathTest.log2 43: [ OK ] SimdMathTest.log2 (0 ms) 43: [ RUN ] SimdMathTest.log 43: [ OK ] SimdMathTest.log (0 ms) 43: [ RUN ] SimdMathTest.exp2 43: [ OK ] SimdMathTest.exp2 (5 ms) 43: [ RUN ] SimdMathTest.exp2Unsafe 43: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 43: [ RUN ] SimdMathTest.exp 43: [ OK ] SimdMathTest.exp (5 ms) 43: [ RUN ] SimdMathTest.expUnsafe 43: [ OK ] SimdMathTest.expUnsafe (1 ms) 43: [ RUN ] SimdMathTest.pow 43: [ OK ] SimdMathTest.pow (0 ms) 43: [ RUN ] SimdMathTest.powUnsafe 43: [ OK ] SimdMathTest.powUnsafe (0 ms) 43: [ RUN ] SimdMathTest.erf 43: [ OK ] SimdMathTest.erf (2 ms) 43: [ RUN ] SimdMathTest.erfc 43: [ OK ] SimdMathTest.erfc (1 ms) 43: [ RUN ] SimdMathTest.sin 43: [ OK ] SimdMathTest.sin (2 ms) 43: [ RUN ] SimdMathTest.cos 43: [ OK ] SimdMathTest.cos (2 ms) 43: [ RUN ] SimdMathTest.tan 43: [ OK ] SimdMathTest.tan (3 ms) 43: [ RUN ] SimdMathTest.asin 43: [ OK ] SimdMathTest.asin (1 ms) 43: [ RUN ] SimdMathTest.acos 43: [ OK ] SimdMathTest.acos (1 ms) 43: [ RUN ] SimdMathTest.atan 43: [ OK ] SimdMathTest.atan (1 ms) 43: [ RUN ] SimdMathTest.atan2 43: [ OK ] SimdMathTest.atan2 (0 ms) 43: [ RUN ] SimdMathTest.pmeForceCorrection 43: [ OK ] SimdMathTest.pmeForceCorrection (1 ms) 43: [ RUN ] SimdMathTest.pmePotentialCorrection 43: [ OK ] SimdMathTest.pmePotentialCorrection (1 ms) 43: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 43: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 43: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.sqrtSingleAccuracy 43: [ OK ] SimdMathTest.sqrtSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 43: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.invSingleAccuracy 43: [ OK ] SimdMathTest.invSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.cbrtSingleAccuracy 43: [ OK ] SimdMathTest.cbrtSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 43: [ OK ] SimdMathTest.invcbrtSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.log2SingleAccuracy 43: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.logSingleAccuracy 43: [ OK ] SimdMathTest.logSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.exp2SingleAccuracy 43: [ OK ] SimdMathTest.exp2SingleAccuracy (4 ms) 43: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 43: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.expSingleAccuracy 43: [ OK ] SimdMathTest.expSingleAccuracy (7 ms) 43: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 43: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.powSingleAccuracy 43: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 43: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.erfSingleAccuracy 43: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.erfcSingleAccuracy 43: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.sinSingleAccuracy 43: [ OK ] SimdMathTest.sinSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.cosSingleAccuracy 43: [ OK ] SimdMathTest.cosSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.tanSingleAccuracy 43: [ OK ] SimdMathTest.tanSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.asinSingleAccuracy 43: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.acosSingleAccuracy 43: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.atanSingleAccuracy 43: [ OK ] SimdMathTest.atanSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.atan2SingleAccuracy 43: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 43: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 43: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 43: [----------] 56 tests from SimdMathTest (100 ms total) 43: 43: [----------] 1 test from EmptyArrayRefTest 43: [ RUN ] EmptyArrayRefTest.IsEmpty 43: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 43: [----------] 1 test from EmptyArrayRefTest (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 43: 43: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefReadWriteTest/0.Assignment 43: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 43: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 43: 43: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefReadWriteTest/1.Assignment 43: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 43: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 43: 43: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefArithmeticTest/0.Basic 43: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 43: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 43: 43: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefArithmeticTest/1.Basic 43: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 43: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 43: 43: [----------] 3 tests from SimdVectorOperationsTest 43: [ RUN ] SimdVectorOperationsTest.iprod 43: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 43: [ RUN ] SimdVectorOperationsTest.norm2 43: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 43: [ RUN ] SimdVectorOperationsTest.cprod 43: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 43: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 247 tests from 19 test suites ran. (103 ms total) 43: [ PASSED ] 247 tests. 43/81 Test #43: SimdUnitTests .................................. Passed 0.14 sec test 44 Start 44: CompatibilityHelpersTests 44: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/compat/tests 44: Test timeout computed to be: 30 44: [==========] Running 9 tests from 6 test suites. 44: [----------] Global test environment set-up. 44: [----------] 4 tests from TemplateMPTest 44: [ RUN ] TemplateMPTest.MpWithIndexInt 44: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 44: [ RUN ] TemplateMPTest.MpWithIndexIntBad 44: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 44: [ RUN ] TemplateMPTest.MpWithIndexBool 44: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 44: [ RUN ] TemplateMPTest.MpWithIndexEnum 44: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 44: [----------] 4 tests from TemplateMPTest (0 ms total) 44: 44: [----------] 1 test from NotNullConstruction 44: [ RUN ] NotNullConstruction.Works 44: [ OK ] NotNullConstruction.Works (0 ms) 44: [----------] 1 test from NotNullConstruction (0 ms total) 44: 44: [----------] 1 test from NotNullCasting 44: [ RUN ] NotNullCasting.Works 44: [ OK ] NotNullCasting.Works (0 ms) 44: [----------] 1 test from NotNullCasting (0 ms total) 44: 44: [----------] 1 test from NotNullAssignment 44: [ RUN ] NotNullAssignment.Works 44: [ OK ] NotNullAssignment.Works (0 ms) 44: [----------] 1 test from NotNullAssignment (0 ms total) 44: 44: [----------] 1 test from MakeNotNull 44: [ RUN ] MakeNotNull.Works 44: [ OK ] MakeNotNull.Works (0 ms) 44: [----------] 1 test from MakeNotNull (0 ms total) 44: 44: [----------] 1 test from NotNull 44: [ RUN ] NotNull.WorksInContainers 44: [ OK ] NotNull.WorksInContainers (0 ms) 44: [----------] 1 test from NotNull (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 9 tests from 6 test suites ran. (0 ms total) 44: [ PASSED ] 9 tests. 44/81 Test #44: CompatibilityHelpersTests ...................... Passed 0.02 sec test 45 Start 45: GmxAnaTest 45: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 45: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxana/tests 45: Test timeout computed to be: 600 45: [==========] Running 22 tests from 4 test suites. 45: [----------] Global test environment set-up. 45: [----------] 5 tests from Entropy 45: [ RUN ] Entropy.Schlitter_300_NoLinear 45: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 45: [ RUN ] Entropy.Schlitter_300_Linear 45: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 45: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 45: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 45: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 45: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 45: [ RUN ] Entropy.QuasiHarmonic_200_Linear 45: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 45: [----------] 5 tests from Entropy (0 ms total) 45: 45: [----------] 1 test from GmxChiTest 45: [ RUN ] GmxChiTest.gmxchiWorksWithAll 45: 45: 10 residues with dihedrals found 45: 46 dihedrals found 45: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 45: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 45: j after resetting (nr. active dihedrals) = 46 45: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 45: Now calculating transitions... 45: Total number of transitions: 0 45: Now printing out transitions and OPs... 45: Now printing out rotamer occupancies... 45: Now calculating Chi product trajectories... 45: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 45: 45: gmx chi is deprecated. 45: See https://gitlab.com/gromacs/gromacs/-/issues/4108 if 45: you are interested in preserving it! 45: [ OK ] GmxChiTest.gmxchiWorksWithAll (1290 ms) 45: [----------] 1 test from GmxChiTest (1440 ms total) 45: 45: [----------] 10 tests from MindistTest 45: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.mindistWorksWithSingleAtoms (22 ms) 45: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 2: 'atom3' 45: Selected 3: 'atoms12' 45: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (9 ms) 45: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.mindistDoesNotPickUpContacts (1 ms) 45: [ RUN ] MindistTest.mindistPicksUpContacts 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.mindistPicksUpContacts (2 ms) 45: [ RUN ] MindistTest.ngWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: Selected 2: 'atom3' 45: [ OK ] MindistTest.ngWorks (0 ms) 45: [ RUN ] MindistTest.groupWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 3: 'atoms12' 45: Selected 2: 'atom3' 45: [ OK ] MindistTest.groupWorks (0 ms) 45: [ RUN ] MindistTest.maxDistWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 2: 'atom3' 45: Selected 3: 'atoms12' 45: [ OK ] MindistTest.maxDistWorks (0 ms) 45: [ RUN ] MindistTest.noPbcWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.noPbcWorks (0 ms) 45: [ RUN ] MindistTest.resPerTimeWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 3: 'atoms12' 45: Selected 2: 'atom3' 45: [ OK ] MindistTest.resPerTimeWorks (0 ms) 45: [ RUN ] MindistTest.matrixWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 5: 'atoms123' 45: Special case: making distance matrix between all atoms in group atoms123 45: [ OK ] MindistTest.matrixWorks (0 ms) 45: [----------] 10 tests from MindistTest (40 ms total) 45: 45: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: trr version: GMX_trn_file (single precision) 45: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (9 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (1 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (1 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 45: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (3 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 45: Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) 45: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (19 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 22 tests from 4 test suites ran. (1501 ms total) 45: [ PASSED ] 22 tests. 45/81 Test #45: GmxAnaTest ..................................... Passed 1.53 sec test 46 Start 46: GmxPreprocessTests 46: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests 46: Test timeout computed to be: 1920 46: [==========] Running 72 tests from 10 test suites. 46: [----------] Global test environment set-up. 46: [----------] 4 tests from GenconfTest 46: [ RUN ] GenconfTest.nbox_Works 46: [ OK ] GenconfTest.nbox_Works (0 ms) 46: [ RUN ] GenconfTest.nbox_norenumber_Works 46: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 46: [ RUN ] GenconfTest.nbox_dist_Works 46: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 46: [ RUN ] GenconfTest.nbox_rot_Works 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 46: [----------] 4 tests from GenconfTest (3 ms total) 46: 46: [----------] 2 tests from GenionTest 46: [ RUN ] GenionTest.HighConcentrationIonPlacement 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 46: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 46: buffer. The cluster pair list does have a buffering effect, but choosing 46: a larger rlist might be necessary for good energy conservation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: Generating 1-4 interactions: fudge = 0.5 46: Number of degrees of freedom in T-Coupling group rest is 1308.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 46: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 46: Group 0 ( System) has 653 elements 46: Group 1 ( Water) has 648 elements 46: Group 2 ( SOL) has 648 elements 46: Group 3 ( non-Water) has 5 elements 46: Group 4 ( Other) has 5 elements 46: Group 5 ( METH) has 5 elements 46: Select a group: Number of (3-atomic) solvent molecules: 216 46: Using random seed 1997. 46: Replacing solvent molecule 56 (atom 168) with NA 46: Replacing solvent molecule 120 (atom 360) with NA 46: Replacing solvent molecule 182 (atom 546) with NA 46: Replacing solvent molecule 71 (atom 213) with NA 46: Replacing solvent molecule 189 (atom 567) with CL 46: Replacing solvent molecule 54 (atom 162) with CL 46: Replacing solvent molecule 155 (atom 465) with CL 46: Replacing solvent molecule 99 (atom 297) with CL 46: 46: Setting the LD random seed to 1744760825 46: 46: Generated 331705 of the 331705 non-bonded parameter combinations 46: 46: Generated 331705 of the 331705 1-4 parameter combinations 46: 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: 46: Excluding 3 bonded neighbours molecule type 'methane' 46: Analysing residue names: 46: There are: 216 Water residues 46: There are: 1 Other residues 46: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 46: 46: This run will generate roughly 0 Mb of data 46: Will try to add 4 NA ions and 4 CL ions. 46: Select a continuous group of solvent molecules 46: Selected 1: 'Water' 46: [ OK ] GenionTest.HighConcentrationIonPlacement (611 ms) 46: [ RUN ] GenionTest.NoIonPlacement 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 46: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 46: buffer. The cluster pair list does have a buffering effect, but choosing 46: a larger rlist might be necessary for good energy conservation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: Generating 1-4 interactions: fudge = 0.5 46: Number of degrees of freedom in T-Coupling group rest is 1308.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 46: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 46: No ions to add, will just copy input configuration. 46: Setting the LD random seed to -1214546691 46: 46: Generated 331705 of the 331705 non-bonded parameter combinations 46: 46: Generated 331705 of the 331705 1-4 parameter combinations 46: 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: 46: Excluding 3 bonded neighbours molecule type 'methane' 46: Analysing residue names: 46: There are: 216 Water residues 46: There are: 1 Other residues 46: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 46: 46: This run will generate roughly 0 Mb of data 46: [ OK ] GenionTest.NoIonPlacement (716 ms) 46: [----------] 2 tests from GenionTest (1328 ms total) 46: 46: [----------] 1 test from GenRestrTest 46: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 46: 46: Reading structure file 46: Group 0 ( System) has 156 elements 46: Group 1 ( Protein) has 156 elements 46: Group 2 ( Protein-H) has 75 elements 46: Group 3 ( C-alpha) has 10 elements 46: Group 4 ( Backbone) has 30 elements 46: Group 5 ( MainChain) has 40 elements 46: Group 6 ( MainChain+Cb) has 49 elements 46: Group 7 ( MainChain+H) has 52 elements 46: Group 8 ( SideChain) has 104 elements 46: Group 9 ( SideChain-H) has 35 elements 46: Select a group: Select group to position restrain 46: Selected 3: 'C-alpha' 46: [ OK ] GenRestrTest.SimpleRestraintsGenerated (8 ms) 46: [----------] 1 test from GenRestrTest (8 ms total) 46: 46: [----------] 9 tests from PreprocessingAtomTypesTest 46: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 46: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 46: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 46: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 46: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 46: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 46: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 46: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 46: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 46: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 46: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 46: 46: [----------] 10 tests from PreprocessingBondAtomTypeTest 46: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 46: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 46: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 46: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 46: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 46: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 46: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 46: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 46: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 46: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 46: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 46: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 46: 46: [----------] 1 test from GromppDirectiveTest 46: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 46: Ignoring obsolete mdp entry 'title' 46: Generating 1-4 interactions: fudge = 0.5 46: 46: NOTE 1 [file directives.top, line 44]: 46: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 46: any other atom in the same moleculetype. Although technically this might 46: not cause issues in a simulation, this often means that the user forgot 46: to add a bond/potential/constraint or put multiple molecules in the same 46: moleculetype definition by mistake. Run with -v to get information for 46: each atom. 46: 46: Number of degrees of freedom in T-Coupling group rest is 9.00 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 46: NVE simulation: will use the initial temperature of 300.000 K for 46: determining the Verlet buffer size 46: 46: 46: There were 2 notes 46: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 46: Setting the LD random seed to -453002257 46: 46: Generated 10 of the 10 non-bonded parameter combinations 46: 46: Generated 10 of the 10 1-4 parameter combinations 46: 46: Excluding 0 bonded neighbours molecule type 'A' 46: 46: Setting gen_seed to -579321869 46: 46: Velocities were taken from a Maxwell distribution at 300 K 46: Analysing residue names: 46: There are: 1 Other residues 46: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 46: 46: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 46: 46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 46: 46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 46: 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: 46: This run will generate roughly 0 Mb of data 46: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (16 ms) 46: [----------] 1 test from GromppDirectiveTest (16 ms total) 46: 46: [----------] 5 tests from InsertMoleculesTest 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 46: Reading solute configuration 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 8 atoms)! 46: 46: Added 1 molecules (out of 1 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 46: 46: Output configuration contains 8 atoms in 4 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 2 atoms)! 46: Try 2 success (now 4 atoms)! 46: Try 3 success (now 6 atoms)! 46: Try 4 success (now 8 atoms)! 46: Try 5 success (now 10 atoms)! 46: 46: Added 5 molecules (out of 5 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 46: 46: Output configuration contains 10 atoms in 10 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (3 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 46: Reading solute configuration 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 8 atoms)! 46: Try 2 success (now 10 atoms)! 46: 46: Added 2 molecules (out of 2 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 46: 46: Output configuration contains 10 atoms in 4 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (1 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 46: Reading solute configuration 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 650 atoms)! 46: Try 2 success (now 652 atoms)! 46: Try 3 success (now 654 atoms)! 46: Try 4 success (now 656 atoms)! 46: 46: Added 4 molecules (out of 4 requested) 46: Replaced 8 residues (24 atoms) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 46: 46: Output configuration contains 632 atoms in 212 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (10 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Read 4 positions from file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 46: 46: Try 1 success (now 2 atoms)! 46: Try 2 success (now 4 atoms)! 46: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 46: Try 13 success (now 6 atoms)! 46: 46: Added 3 molecules (out of 4 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 46: 46: Output configuration contains 6 atoms in 3 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (2 ms) 46: [----------] 5 tests from InsertMoleculesTest (21 ms total) 46: 46: [----------] 34 tests from GetIrTest 46: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 46: Ignoring obsolete mdp entry 'title' 46: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (4 ms) 46: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 46: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (25 ms) 46: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsKeyWithoutValue (4 ms) 46: [ RUN ] GetIrTest.RejectsValueWithoutKey 46: [ OK ] GetIrTest.RejectsValueWithoutKey (31 ms) 46: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 46: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (24 ms) 46: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (8 ms) 46: [ RUN ] GetIrTest.AcceptsEmptyLines 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsEmptyLines (11 ms) 46: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 46: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.MtsCheckNstcalcenergy (2 ms) 46: [ RUN ] GetIrTest.MtsCheckNstenergy 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 46: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (5) 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.MtsCheckNstenergy (6 ms) 46: [ RUN ] GetIrTest.MtsCheckNstpcouple 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 46: Pressure coupling incorrect number of values (I need exactly 1) 46: 46: 46: ERROR 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 46: Pressure coupling incorrect number of values (I need exactly 1) 46: 46: 46: ERROR 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: With multiple time stepping, nstpcouple should be a mutiple of mts-factor 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: 46: ERROR 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: The Berendsen barostat does not generate any strictly correct ensemble, 46: and should not be used for new production simulations (in our opinion). 46: For isotropic scaling we would recommend the C-rescale barostat that also 46: ensures fast relaxation without oscillations, and for anisotropic scaling 46: you likely want to use the Parrinello-Rahman barostat. 46: 46: 46: ERROR 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: compressibility must be > 0 when using pressure coupling Berendsen 46: 46: 46: [ OK ] GetIrTest.MtsCheckNstpcouple (10 ms) 46: [ RUN ] GetIrTest.MtsCheckNstdhdl 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstdhdl (5) 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: 46: ERROR 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: Lambda state must be set, either with init-lambda-state or with 46: init-lambda 46: 46: [ OK ] GetIrTest.MtsCheckNstdhdl (2 ms) 46: [ RUN ] GetIrTest.AcceptsElectricField 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsElectricField (12 ms) 46: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (3 ms) 46: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (11 ms) 46: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 46: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (29 ms) 46: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsImplicitSolventNo (4 ms) 46: [ RUN ] GetIrTest.RejectsImplicitSolventYes 46: [ OK ] GetIrTest.RejectsImplicitSolventYes (31 ms) 46: [ RUN ] GetIrTest.AcceptsMimic 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsMimic (4 ms) 46: [ RUN ] GetIrTest.AcceptsTransformationCoord 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 46: pull-coord2 has a non-zero force constant and is also referenced in 46: pull-coord1-expression. Make sure that this is intended. In most use 46: cases, the pull coordinates referenced by a transformation coordinate 46: should have their force constant set to zero. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsTransformationCoord (11 ms) 46: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 46: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (2 ms) 46: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 46: pull-coord2 can not use pull-coord1 in the transformation since this is a 46: constraint 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (7 ms) 46: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 46: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 46: 'transformation' 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (11 ms) 46: [ RUN ] GetIrTest.MissingTransformationCoordExpression 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 46: pull-coord1-expression not set for pull coordinate of geometry 46: 'transformation' 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.MissingTransformationCoordExpression (6 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (6 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (10 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (7 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 46: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 46: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 46: in total 100001 steps. This is not compatible with using soft-core 46: potentials. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 46: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 46: won't change anymore after step 100000 until the end of the simulation 46: after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (6 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 46: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 46: won't change anymore after step 100000 until the end of the simulation 46: after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 46: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 46: components won't change anymore after step 100000 until the end of the 46: simulation after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (10 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 46: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 46: components won't change anymore after step 100000 until the end of the 46: simulation after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (6 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (10 ms) 46: [----------] 34 tests from GetIrTest (340 ms total) 46: 46: [----------] 5 tests from SolvateTest 46: [ RUN ] SolvateTest.cs_box_Works 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 1x1x1 boxes 46: Solvent box contains 270 atoms in 90 residues 46: Removed 129 solvent atoms due to solvent-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 47 residues 46: Generated solvent containing 141 atoms in 47 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 46: 46: Output configuration contains 141 atoms in 47 residues 46: Volume : 1.331 (nm^3) 46: Density : 1056.36 (g/l) 46: Number of solvent molecules: 47 46: 46: [ OK ] SolvateTest.cs_box_Works (17 ms) 46: [ RUN ] SolvateTest.cs_cp_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 2x2x2 boxes 46: Solvent box contains 3660 atoms in 1220 residues 46: Removed 987 solvent atoms due to solvent-solvent overlap 46: Removed 15 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 886 residues 46: Generated solvent containing 2658 atoms in 886 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 46: 46: Output configuration contains 2664 atoms in 888 residues 46: Volume : 27.2709 (nm^3) 46: Density : 974.777 (g/l) 46: Number of solvent molecules: 886 46: 46: [ OK ] SolvateTest.cs_cp_Works (92 ms) 46: [ RUN ] SolvateTest.cs_cp_p_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 2x2x2 boxes 46: Solvent box contains 3660 atoms in 1220 residues 46: Removed 987 solvent atoms due to solvent-solvent overlap 46: Removed 15 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 886 residues 46: Generated solvent containing 2658 atoms in 886 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 46: 46: Output configuration contains 2664 atoms in 888 residues 46: Volume : 27.2709 (nm^3) 46: Density : 974.777 (g/l) 46: Number of solvent molecules: 886 46: 46: Processing topology 46: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 46: [ OK ] SolvateTest.cs_cp_p_Works (115 ms) 46: [ RUN ] SolvateTest.shell_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 2x2x2 boxes 46: Solvent box contains 3660 atoms in 1220 residues 46: Removed 987 solvent atoms due to solvent-solvent overlap 46: Removed 1902 solvent atoms more than 1.000000 nm from solute. 46: Removed 15 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 252 residues 46: Generated solvent containing 756 atoms in 252 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 46: 46: Output configuration contains 762 atoms in 254 residues 46: Volume : 27.2709 (nm^3) 46: Density : 279.3 (g/l) 46: Number of solvent molecules: 252 46: 46: [ OK ] SolvateTest.shell_Works (58 ms) 46: [ RUN ] SolvateTest.update_Topology_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 3x3x3 boxes 46: Solvent box contains 14952 atoms in 4984 residues 46: Removed 2787 solvent atoms due to solvent-solvent overlap 46: Removed 30 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 2 different molecule types: 46: HOH ( 3 atoms): 1876 residues 46: SOL ( 3 atoms): 2169 residues 46: Generated solvent containing 0 atoms in 0 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 46: 46: Output configuration contains 12141 atoms in 4047 residues 46: Volume : 125 (nm^3) 46: Density : 968.963 (g/l) 46: Number of solvent molecules: 4045 46: 46: Processing topology 46: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 46: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 46: [ OK ] SolvateTest.update_Topology_Works (518 ms) 46: [----------] 5 tests from SolvateTest (803 ms total) 46: 46: [----------] 1 test from TopDirTests 46: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 46: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 46: [----------] 1 test from TopDirTests (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 72 tests from 10 test suites ran. (2521 ms total) 46: [ PASSED ] 72 tests. 46/81 Test #46: GmxPreprocessTests ............................. Passed 2.57 sec test 47 Start 47: Pdb2gmx1Test 47: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 47: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests 47: Test timeout computed to be: 1920 47: [==========] Running 30 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 30 tests from Oplsaa/Pdb2gmxTest 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 0 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (59 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 0 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (57 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 0 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (53 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 0 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (43 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 0 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (258 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Marked 124 virtual sites 47: Added 16 dummy masses 47: Added 26 new constraints 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 130 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (55 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Marked 132 virtual sites 47: Added 10 dummy masses 47: Added 19 new constraints 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 133 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (84 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Marked 123 virtual sites 47: Added 22 dummy masses 47: Added 35 new constraints 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 132 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (59 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Marked 111 virtual sites 47: Added 18 dummy masses 47: Added 31 new constraints 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 116 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (88 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Marked 447 virtual sites 47: Added 58 dummy masses 47: Added 101 new constraints 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 462 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (321 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 0 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (46 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 0 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (55 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 0 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (47 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 0 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (44 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 0 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (215 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Marked 124 virtual sites 47: Added 16 dummy masses 47: Added 26 new constraints 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 130 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (52 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Marked 132 virtual sites 47: Added 10 dummy masses 47: Added 19 new constraints 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 133 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (75 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Marked 123 virtual sites 47: Added 22 dummy masses 47: Added 35 new constraints 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 132 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (51 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Marked 111 virtual sites 47: Added 18 dummy masses 47: Added 31 new constraints 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 116 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (48 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Marked 447 virtual sites 47: Added 58 dummy masses 47: Added 101 new constraints 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 462 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (262 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 0 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (77 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 0 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (89 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 0 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (75 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 0 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (49 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 0 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (294 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Marked 124 virtual sites 47: Added 16 dummy masses 47: Added 26 new constraints 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 130 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (50 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Marked 132 virtual sites 47: Added 10 dummy masses 47: Added 19 new constraints 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 133 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (59 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Marked 123 virtual sites 47: Added 22 dummy masses 47: Added 35 new constraints 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 132 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (52 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Marked 111 virtual sites 47: Added 18 dummy masses 47: Added 31 new constraints 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 116 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge 0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (47 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Marked 447 virtual sites 47: Added 58 dummy masses 47: Added 101 new constraints 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 462 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (348 ms) 47: [----------] 30 tests from Oplsaa/Pdb2gmxTest (3130 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 30 tests from 1 test suite ran. (3130 ms total) 47: [ PASSED ] 30 tests. 47/81 Test #47: Pdb2gmx1Test ................................... Passed 3.19 sec test 48 Start 48: Pdb2gmx2Test 48: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 48: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests 48: Test timeout computed to be: 1920 48: [==========] Running 40 tests from 2 test suites. 48: [----------] Global test environment set-up. 48: [----------] 20 tests from G43a1/Pdb2gmxTest 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (53 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (59 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (81 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (90 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (161 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 37 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 37 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (63 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 53 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 51 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (98 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 36 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 36 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (67 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 33 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 31 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (48 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 146 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 137 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (134 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (56 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (120 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (49 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (57 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (177 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 37 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 37 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (56 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 53 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 51 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (54 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 36 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 36 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (49 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 33 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 31 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (48 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 146 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 137 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (147 ms) 48: [----------] 20 tests from G43a1/Pdb2gmxTest (1679 ms total) 48: 48: [----------] 20 tests from G53a6/Pdb2gmxTest 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (98 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (139 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (128 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (120 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (323 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 39 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 39 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (127 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 57 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 55 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (134 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 38 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 38 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (88 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 35 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 33 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (78 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 150 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 141 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (195 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (92 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (98 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (69 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (78 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (175 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 39 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 39 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (70 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 57 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 55 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (74 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 38 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 38 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (71 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 35 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 33 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (76 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 150 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 141 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (309 ms) 48: [----------] 20 tests from G53a6/Pdb2gmxTest (2556 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 40 tests from 2 test suites ran. (4236 ms total) 48: [ PASSED ] 40 tests. 48/81 Test #48: Pdb2gmx2Test ................................... Passed 4.26 sec test 49 Start 49: Pdb2gmx3Test 49: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 49: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/gmxpreprocess/tests 49: Test timeout computed to be: 1920 49: [==========] Running 39 tests from 6 test suites. 49: [----------] Global test environment set-up. 49: [----------] 10 tests from Amber/Pdb2gmxTest 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 653 pairs 49: Before cleaning: 691 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 255, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 691 dihedrals, 51 impropers, 457 angles 49: 650 pairs, 254 bonds and 0 virtual sites 49: 49: Total mass 1846.132 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (175 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 748 pairs 49: Before cleaning: 788 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 291, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 788 dihedrals, 72 impropers, 516 angles 49: 736 pairs, 290 bonds and 0 virtual sites 49: 49: Total mass 2088.366 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (192 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 676 pairs 49: Before cleaning: 727 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 262, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 727 dihedrals, 56 impropers, 472 angles 49: 667 pairs, 261 bonds and 0 virtual sites 49: 49: Total mass 1861.124 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (182 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 603 pairs 49: Before cleaning: 634 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 233, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 634 dihedrals, 48 impropers, 419 angles 49: 597 pairs, 232 bonds and 0 virtual sites 49: 49: Total mass 1662.888 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (159 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 2499 pairs 49: Before cleaning: 2631 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 952, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2631 dihedrals, 208 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 0 virtual sites 49: 49: Total mass 6908.576 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (662 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 124 virtual sites 49: Added 16 dummy masses 49: Added 26 new constraints 49: Before cleaning: 653 pairs 49: Before cleaning: 691 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 255, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 691 dihedrals, 51 impropers, 457 angles 49: 650 pairs, 254 bonds and 130 virtual sites 49: 49: Total mass 1846.132 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (197 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 132 virtual sites 49: Added 10 dummy masses 49: Added 19 new constraints 49: Before cleaning: 748 pairs 49: Before cleaning: 788 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 291, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 788 dihedrals, 72 impropers, 516 angles 49: 736 pairs, 290 bonds and 133 virtual sites 49: 49: Total mass 2088.366 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (114 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 123 virtual sites 49: Added 22 dummy masses 49: Added 35 new constraints 49: Before cleaning: 676 pairs 49: Before cleaning: 727 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 262, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 727 dihedrals, 56 impropers, 472 angles 49: 667 pairs, 261 bonds and 132 virtual sites 49: 49: Total mass 1861.124 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (123 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 111 virtual sites 49: Added 18 dummy masses 49: Added 31 new constraints 49: Before cleaning: 603 pairs 49: Before cleaning: 634 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 233, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 634 dihedrals, 48 impropers, 419 angles 49: 597 pairs, 232 bonds and 116 virtual sites 49: 49: Total mass 1662.888 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (82 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 447 virtual sites 49: Added 58 dummy masses 49: Added 101 new constraints 49: Before cleaning: 2499 pairs 49: Before cleaning: 2631 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 952, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2631 dihedrals, 208 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 462 virtual sites 49: 49: Total mass 6908.576 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (618 ms) 49: [----------] 10 tests from Amber/Pdb2gmxTest (2509 ms total) 49: 49: [----------] 1 test from AmberTip4p/Pdb2gmxTest 49: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 49: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 2 4 (only water) 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (4 atoms, 2 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 2 residues with 8 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 4, now 4 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 2 angles 49: 0 pairs, 4 bonds and 0 virtual sites 49: 49: Total mass 36.032 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 49: 49: The Amber99sb-ildn force field and the tip4p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (68 ms) 49: [----------] 1 test from AmberTip4p/Pdb2gmxTest (68 ms total) 49: 49: [----------] 12 tests from Charmm/Pdb2gmxTest 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 653 pairs 49: Before cleaning: 663 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 254, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 663 dihedrals, 48 impropers, 457 angles 49: 650 pairs, 254 bonds and 0 virtual sites 49: 49: Total mass 1846.115 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (166 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 748 pairs 49: Before cleaning: 778 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus PHE-33: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 290, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 778 dihedrals, 49 impropers, 516 angles 49: 736 pairs, 290 bonds and 0 virtual sites 49: 49: Total mass 2088.361 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (83 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 676 pairs 49: Before cleaning: 696 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: Start terminus ALA-34: NH3+ 49: End terminus ALA-49: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 261, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 696 dihedrals, 39 impropers, 472 angles 49: 667 pairs, 261 bonds and 0 virtual sites 49: 49: Total mass 1861.130 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (171 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 603 pairs 49: Before cleaning: 618 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: Start terminus LYS-50: NH3+ 49: End terminus PRO-65: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 232, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 618 dihedrals, 38 impropers, 419 angles 49: 597 pairs, 232 bonds and 0 virtual sites 49: 49: Total mass 1662.885 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (158 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 2499 pairs 49: Before cleaning: 2524 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: Start terminus ASN-24: NH3+ 49: End terminus ARG-81: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 951, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 56 cmap torsion pairs 49: 49: There are 2524 dihedrals, 149 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 0 virtual sites 49: 49: Total mass 6908.566 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (473 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 39 pairs 49: Before cleaning: 39 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb... 49: Read 'GLU', 9 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 49: 49: chain #res #atoms 49: 49: 1 'X' 1 9 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'X' (9 atoms, 1 residues) 49: 49: Identified residue GLU1 as a starting terminus. 49: 49: Identified residue GLU1 as a ending terminus. 49: Start terminus GLU-1: NH3+ 49: End terminus GLU-1: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 1 residues with 18 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 17, now 17 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 39 dihedrals, 2 impropers, 30 angles 49: 39 pairs, 17 bonds and 0 virtual sites 49: 49: Total mass 146.123 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (34 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 124 virtual sites 49: Added 16 dummy masses 49: Added 26 new constraints 49: Before cleaning: 653 pairs 49: Before cleaning: 663 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 254, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 663 dihedrals, 48 impropers, 457 angles 49: 650 pairs, 254 bonds and 130 virtual sites 49: 49: Total mass 1846.115 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (79 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 132 virtual sites 49: Added 10 dummy masses 49: Added 19 new constraints 49: Before cleaning: 748 pairs 49: Before cleaning: 778 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus PHE-33: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 290, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 778 dihedrals, 49 impropers, 516 angles 49: 736 pairs, 290 bonds and 133 virtual sites 49: 49: Total mass 2088.361 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (87 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 123 virtual sites 49: Added 22 dummy masses 49: Added 35 new constraints 49: Before cleaning: 676 pairs 49: Before cleaning: 696 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: Start terminus ALA-34: NH3+ 49: End terminus ALA-49: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 261, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 696 dihedrals, 39 impropers, 472 angles 49: 667 pairs, 261 bonds and 132 virtual sites 49: 49: Total mass 1861.130 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (90 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 111 virtual sites 49: Added 18 dummy masses 49: Added 31 new constraints 49: Before cleaning: 603 pairs 49: Before cleaning: 618 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: Start terminus LYS-50: NH3+ 49: End terminus PRO-65: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 232, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 618 dihedrals, 38 impropers, 419 angles 49: 597 pairs, 232 bonds and 116 virtual sites 49: 49: Total mass 1662.885 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (80 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 447 virtual sites 49: Added 58 dummy masses 49: Added 101 new constraints 49: Before cleaning: 2499 pairs 49: Before cleaning: 2524 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: Start terminus ASN-24: NH3+ 49: End terminus ARG-81: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 951, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 56 cmap torsion pairs 49: 49: There are 2524 dihedrals, 149 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 462 virtual sites 49: 49: Total mass 6908.566 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (345 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 8 virtual sites 49: Added 2 dummy masses 49: Added 3 new constraints 49: Before cleaning: 39 pairs 49: Before cleaning: 39 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb... 49: Read 'GLU', 9 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 49: 49: chain #res #atoms 49: 49: 1 'X' 1 9 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'X' (9 atoms, 1 residues) 49: 49: Identified residue GLU1 as a starting terminus. 49: 49: Identified residue GLU1 as a ending terminus. 49: Start terminus GLU-1: NH3+ 49: End terminus GLU-1: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 1 residues with 18 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 17, now 17 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 39 dihedrals, 2 impropers, 30 angles 49: 39 pairs, 17 bonds and 9 virtual sites 49: 49: Total mass 146.123 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (46 ms) 49: [----------] 12 tests from Charmm/Pdb2gmxTest (1820 ms total) 49: 49: [----------] 8 tests from ChainSep/Pdb2gmxTest 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 651 pairs 49: Before cleaning: 661 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on changing chain id only (ignoring TER records). 49: 49: Merged chains into joint molecule definitions at 2 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: Start terminus PHE-6: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 258 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 258, now 258 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 10 cmap torsion pairs 49: 49: There are 661 dihedrals, 46 impropers, 463 angles 49: 648 pairs, 258 bonds and 0 virtual sites 49: 49: Total mass 1882.146 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (100 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 123 pairs 49: Before cleaning: 123 dihedrals 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 10 donors and 7 acceptors were found. 49: There are 7 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS8 49: NE223 49: MET12 SD55 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 317 pairs 49: Before cleaning: 322 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on changing chain id only (ignoring TER records). 49: 49: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 4 28 49: 49: 2 'B' 7 58 49: 49: 3 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (28 atoms, 4 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 4 residues with 51 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 50, now 50 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2 cmap torsion pairs 49: 49: There are 123 dihedrals, 9 impropers, 88 angles 49: 123 pairs, 50 bonds and 0 virtual sites 49: 49: Total mass 434.421 a.m.u. 49: 49: Total charge -2.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (58 atoms, 7 residues) 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus PHE-6: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 7 residues with 124 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 125, now 125 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 5 cmap torsion pairs 49: 49: There are 322 dihedrals, 19 impropers, 227 angles 49: 314 pairs, 125 bonds and 0 virtual sites 49: 49: Total mass 846.083 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 51 atoms 4 residues 49: 49: Including chain 2 in system: 124 atoms 7 residues 49: 49: Including chain 3 in system: 83 atoms 5 residues 49: 49: Now there are 258 atoms and 16 residues 49: 49: Total mass in system 1882.146 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (71 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 651 pairs 49: Before cleaning: 661 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records only (ignoring chain id). 49: 49: Merged chains into joint molecule definitions at 2 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ILE-9: COO- 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 258 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 258, now 258 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 10 cmap torsion pairs 49: 49: There are 661 dihedrals, 46 impropers, 463 angles 49: 648 pairs, 258 bonds and 0 virtual sites 49: 49: Total mass 1882.146 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (81 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 10 donors and 12 acceptors were found. 49: There are 13 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 49: SG9 49: HIS8 NE251 1.055 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 288 pairs 49: Before cleaning: 293 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 152 pairs 49: Before cleaning: 152 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records only (ignoring chain id). 49: 49: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 8 61 49: 49: 2 'B' 3 25 49: 49: 3 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (61 atoms, 8 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ILE-9: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 8 residues with 114 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 115, now 115 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 6 cmap torsion pairs 49: 49: There are 293 dihedrals, 23 impropers, 203 angles 49: 285 pairs, 115 bonds and 0 virtual sites 49: 49: Total mass 888.952 a.m.u. 49: 49: Total charge -2.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (25 atoms, 3 residues) 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 61 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 60, now 60 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 152 dihedrals, 5 impropers, 112 angles 49: 152 pairs, 60 bonds and 0 virtual sites 49: 49: Total mass 391.552 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 114 atoms 8 residues 49: 49: Including chain 2 in system: 61 atoms 3 residues 49: 49: Including chain 3 in system: 83 atoms 5 residues 49: 49: Now there are 258 atoms and 16 residues 49: 49: Total mass in system 1882.146 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (64 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 650 pairs 49: Before cleaning: 660 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Merged chains into joint molecule definitions at 3 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: Start terminus PHE-6: NH3+ 49: End terminus ILE-9: COO- 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 261 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 260, now 260 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 8 cmap torsion pairs 49: 49: There are 660 dihedrals, 45 impropers, 466 angles 49: 647 pairs, 260 bonds and 0 virtual sites 49: 49: Total mass 1900.162 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (106 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 123 pairs 49: Before cleaning: 123 dihedrals 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 6 donors and 4 acceptors were found. 49: There are 3 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 164 pairs 49: Before cleaning: 169 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 152 pairs 49: Before cleaning: 152 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 4 28 49: 49: 2 'B' 4 33 49: 49: 3 'B' 3 25 49: 49: 4 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (28 atoms, 4 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 4 residues with 51 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 50, now 50 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2 cmap torsion pairs 49: 49: There are 123 dihedrals, 9 impropers, 88 angles 49: 123 pairs, 50 bonds and 0 virtual sites 49: 49: Total mass 434.421 a.m.u. 49: 49: Total charge -2.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (33 atoms, 4 residues) 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: Start terminus PHE-6: NH3+ 49: End terminus ILE-9: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 4 residues with 66 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 67, now 67 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2 cmap torsion pairs 49: 49: There are 169 dihedrals, 13 impropers, 118 angles 49: 161 pairs, 67 bonds and 0 virtual sites 49: 49: Total mass 472.547 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'B' (25 atoms, 3 residues) 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 61 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 60, now 60 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 152 dihedrals, 5 impropers, 112 angles 49: 152 pairs, 60 bonds and 0 virtual sites 49: 49: Total mass 391.552 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Processing chain 4 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 51 atoms 4 residues 49: 49: Including chain 2 in system: 66 atoms 4 residues 49: 49: Including chain 3 in system: 61 atoms 3 residues 49: 49: Including chain 4 in system: 83 atoms 5 residues 49: 49: Now there are 261 atoms and 16 residues 49: 49: Total mass in system 1900.162 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (68 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 652 pairs 49: Before cleaning: 662 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records and chain id changing. 49: 49: Merged chains into joint molecule definitions at 1 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 256, now 256 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 12 cmap torsion pairs 49: 49: There are 662 dihedrals, 47 impropers, 460 angles 49: 649 pairs, 256 bonds and 0 virtual sites 49: 49: Total mass 1864.131 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (81 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 14 donors and 15 acceptors were found. 49: There are 20 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 441 pairs 49: Before cleaning: 446 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records and chain id changing. 49: 49: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 11 86 49: 49: 2 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (86 atoms, 11 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 11 residues with 172 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 173, now 173 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 9 cmap torsion pairs 49: 49: There are 446 dihedrals, 29 impropers, 312 angles 49: 438 pairs, 173 bonds and 0 virtual sites 49: 49: Total mass 1262.488 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 172 atoms 11 residues 49: 49: Including chain 2 in system: 83 atoms 5 residues 49: 49: Now there are 255 atoms and 16 residues 49: 49: Total mass in system 1864.131 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (70 ms) 49: [----------] 8 tests from ChainSep/Pdb2gmxTest (645 ms total) 49: 49: [----------] 4 tests from ChainChanges/Pdb2gmxTest 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on changing chain id only (ignoring TER records). 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (46 ms) 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records only (ignoring chain id). 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (48 ms) 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (45 ms) 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records and chain id changing. 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (45 ms) 49: [----------] 4 tests from ChainChanges/Pdb2gmxTest (185 ms total) 49: 49: [----------] 4 tests from Cyclic/Pdb2gmxTest 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: WARNING: all CONECT records are ignored 49: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 6040 pairs 49: Before cleaning: 6605 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 6040 pairs 49: Before cleaning: 6605 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 49: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: Moved all the water blocks to the end 49: 49: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 49: 49: chain #res #atoms 49: 49: 1 'P' 71 1527 49: 49: 2 'Q' 71 1527 49: 49: 3 'Q' 7 7 49: 49: 4 ' ' 10 10 (only water) 49: 49: 5 ' ' 16 16 (only water) 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'P' (1527 atoms, 71 residues) 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 71 residues with 2297 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 2481, now 2481 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 6605 dihedrals, 183 impropers, 4434 angles 49: 5827 pairs, 2481 bonds and 0 virtual sites 49: 49: Total mass 22984.514 a.m.u. 49: 49: Total charge -71.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'Q' (1527 atoms, 71 residues) 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 71 residues with 2297 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 2481, now 2481 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 6605 dihedrals, 183 impropers, 4434 angles 49: 5827 pairs, 2481 bonds and 0 virtual sites 49: 49: Total mass 22984.514 a.m.u. 49: 49: Total charge -71.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'Q' (7 atoms, 7 residues) 49: 49: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 49: 49: Disabling further notes about ions. 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 7 residues with 7 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: No bonds 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 0 angles 49: 0 pairs, 0 bonds and 0 virtual sites 49: 49: Total mass 170.135 a.m.u. 49: 49: Total charge 14.000 e 49: 49: Writing topology 49: 49: Processing chain 4 (10 atoms, 10 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 10 residues with 30 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 30, now 30 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 30 angles 49: 0 pairs, 30 bonds and 0 virtual sites 49: 49: Total mass 180.154 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Processing chain 5 (16 atoms, 16 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 48 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 48, now 48 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 48 angles 49: 0 pairs, 48 bonds and 0 virtual sites 49: 49: Total mass 288.246 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Including chain 1 in system: 2297 atoms 71 residues 49: 49: Including chain 2 in system: 2297 atoms 71 residues 49: 49: Including chain 3 in system: 7 atoms 7 residues 49: 49: Including chain 4 in system: 30 atoms 10 residues 49: 49: Including chain 5 in system: 48 atoms 16 residues 49: 49: Now there are 4679 atoms and 175 residues 49: 49: Total mass in system 46607.563 a.m.u. 49: 49: Total charge in system -128.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (3440 ms) 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 2325 pairs 49: Before cleaning: 2325 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 49: Read 'CARNOCYCLIN-A', 413 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 60 413 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (413 atoms, 60 residues) 49: 49: Identified residue LEU1 as a starting terminus. 49: 49: Identified residue LEU60 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 60 residues with 878 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 880, now 880 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 60 cmap torsion pairs 49: 49: There are 2325 dihedrals, 137 impropers, 1614 angles 49: 2319 pairs, 880 bonds and 0 virtual sites 49: 49: Total mass 5866.087 a.m.u. 49: 49: Total charge 4.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (290 ms) 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: WARNING: all CONECT records are ignored 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 12080 pairs 49: Before cleaning: 13210 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 49: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Moved all the water blocks to the end 49: 49: Merged chains into joint molecule definitions at 2 places. 49: 49: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 49: 49: chain #res #atoms 49: 49: 1 'P' 149 3061 49: 49: 2 ' ' 10 10 (only water) 49: 49: 3 ' ' 16 16 (only water) 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'P' (3061 atoms, 149 residues) 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 49: 49: Disabling further notes about ions. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 149 residues with 4601 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 4962, now 4962 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 13210 dihedrals, 366 impropers, 8868 angles 49: 11654 pairs, 4962 bonds and 0 virtual sites 49: 49: Total mass 46139.162 a.m.u. 49: 49: Total charge -128.000 e 49: 49: Writing topology 49: 49: Processing chain 2 (10 atoms, 10 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 10 residues with 30 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 30, now 30 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 30 angles 49: 0 pairs, 30 bonds and 0 virtual sites 49: 49: Total mass 180.154 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Processing chain 3 (16 atoms, 16 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 48 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 48, now 48 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 48 angles 49: 0 pairs, 48 bonds and 0 virtual sites 49: 49: Total mass 288.246 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Including chain 1 in system: 4601 atoms 149 residues 49: 49: Including chain 2 in system: 30 atoms 10 residues 49: 49: Including chain 3 in system: 48 atoms 16 residues 49: 49: Now there are 4679 atoms and 175 residues 49: 49: Total mass in system 46607.563 a.m.u. 49: 49: Total charge in system -128.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (6533 ms) 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 2325 pairs 49: Before cleaning: 2325 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 49: Read 'CARNOCYCLIN-A', 413 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 60 413 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (413 atoms, 60 residues) 49: 49: Identified residue LEU1 as a starting terminus. 49: 49: Identified residue LEU60 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 60 residues with 878 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 880, now 880 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 60 cmap torsion pairs 49: 49: There are 2325 dihedrals, 137 impropers, 1614 angles 49: 2319 pairs, 880 bonds and 0 virtual sites 49: 49: Total mass 5866.087 a.m.u. 49: 49: Total charge 4.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (320 ms) 49: [----------] 4 tests from Cyclic/Pdb2gmxTest (10585 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 39 tests from 6 test suites ran. (15814 ms total) 49: [ PASSED ] 39 tests. 49/81 Test #49: Pdb2gmx3Test ................................... Passed 15.89 sec test 50 Start 50: CorrelationsTest 50: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/correlationfunctions/tests 50: Test timeout computed to be: 30 50: [==========] Running 21 tests from 3 test suites. 50: [----------] Global test environment set-up. 50: [----------] 10 tests from AutocorrTest 50: [ RUN ] AutocorrTest.EacNormal 50: [ OK ] AutocorrTest.EacNormal (141 ms) 50: [ RUN ] AutocorrTest.EacNoNormalize 50: [ OK ] AutocorrTest.EacNoNormalize (83 ms) 50: [ RUN ] AutocorrTest.EacCos 50: [ OK ] AutocorrTest.EacCos (139 ms) 50: [ RUN ] AutocorrTest.EacVector 50: [ OK ] AutocorrTest.EacVector (183 ms) 50: [ RUN ] AutocorrTest.EacRcross 50: [ OK ] AutocorrTest.EacRcross (1 ms) 50: [ RUN ] AutocorrTest.EacP0 50: [ OK ] AutocorrTest.EacP0 (181 ms) 50: [ RUN ] AutocorrTest.EacP1 50: [ OK ] AutocorrTest.EacP1 (219 ms) 50: [ RUN ] AutocorrTest.EacP2 50: [ OK ] AutocorrTest.EacP2 (391 ms) 50: [ RUN ] AutocorrTest.EacP3 50: [ OK ] AutocorrTest.EacP3 (12 ms) 50: [ RUN ] AutocorrTest.EacP4 50: [ OK ] AutocorrTest.EacP4 (183 ms) 50: [----------] 10 tests from AutocorrTest (1541 ms total) 50: 50: [----------] 10 tests from ExpfitTest 50: [ RUN ] ExpfitTest.EffnEXP1 50: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 50: [ RUN ] ExpfitTest.EffnEXP2 50: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 50: [ RUN ] ExpfitTest.EffnEXPEXP 50: [ OK ] ExpfitTest.EffnEXPEXP (1 ms) 50: [ RUN ] ExpfitTest.EffnEXP5 50: [ OK ] ExpfitTest.EffnEXP5 (21 ms) 50: [ RUN ] ExpfitTest.EffnEXP7 50: [ OK ] ExpfitTest.EffnEXP7 (9 ms) 50: [ RUN ] ExpfitTest.EffnEXP9 50: [ OK ] ExpfitTest.EffnEXP9 (43 ms) 50: [ RUN ] ExpfitTest.EffnERF 50: [ OK ] ExpfitTest.EffnERF (10 ms) 50: [ RUN ] ExpfitTest.EffnERREST 50: [ OK ] ExpfitTest.EffnERREST (11 ms) 50: [ RUN ] ExpfitTest.EffnVAC 50: [ OK ] ExpfitTest.EffnVAC (16 ms) 50: [ RUN ] ExpfitTest.EffnPRES 50: [ OK ] ExpfitTest.EffnPRES (44 ms) 50: [----------] 10 tests from ExpfitTest (161 ms total) 50: 50: [----------] 1 test from ManyAutocorrelationTest 50: [ RUN ] ManyAutocorrelationTest.Empty 50: [ OK ] ManyAutocorrelationTest.Empty (6 ms) 50: [----------] 1 test from ManyAutocorrelationTest (6 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 21 tests from 3 test suites ran. (1723 ms total) 50: [ PASSED ] 21 tests. 50/81 Test #50: CorrelationsTest ............................... Passed 1.78 sec test 51 Start 51: AnalysisDataUnitTests 51: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/analysisdata/tests 51: Test timeout computed to be: 30 51: [==========] Running 69 tests from 14 test suites. 51: [----------] Global test environment set-up. 51: [----------] 3 tests from AnalysisDataInitializationTest 51: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 51: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 51: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 51: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 51: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 51: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 51: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 51: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (8 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/0 (12 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 51: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (8 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/1 (12 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 51: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 51: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (8 ms) 51: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/2 (13 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 51: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 51: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/3 (9 ms total) 51: 51: [----------] 4 tests from AnalysisArrayDataTest 51: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 51: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisArrayDataTest.StorageWorks 51: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 51: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 51: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 51: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 51: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 51: [----------] 4 tests from AnalysisArrayDataTest (1 ms total) 51: 51: [----------] 6 tests from AverageModuleTest 51: [ RUN ] AverageModuleTest.BasicTest 51: [ OK ] AverageModuleTest.BasicTest (9 ms) 51: [ RUN ] AverageModuleTest.HandlesMultipointData 51: [ OK ] AverageModuleTest.HandlesMultipointData (1 ms) 51: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 51: [ OK ] AverageModuleTest.HandlesMultipleDataSets (1 ms) 51: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 51: [ OK ] AverageModuleTest.HandlesDataSetAveraging (1 ms) 51: [ RUN ] AverageModuleTest.CanCustomizeXAxis 51: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 51: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 51: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 51: [----------] 6 tests from AverageModuleTest (14 ms total) 51: 51: [----------] 2 tests from FrameAverageModuleTest 51: [ RUN ] FrameAverageModuleTest.BasicTest 51: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 51: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 51: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (9 ms) 51: [----------] 2 tests from FrameAverageModuleTest (10 ms total) 51: 51: [----------] 7 tests from AnalysisHistogramSettingsTest 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 51: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 51: 51: [----------] 2 tests from SimpleHistogramModuleTest 51: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 51: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (1 ms) 51: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 51: [----------] 2 tests from SimpleHistogramModuleTest (2 ms total) 51: 51: [----------] 3 tests from WeightedHistogramModuleTest 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (5 ms) 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 51: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 51: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (9 ms) 51: [----------] 3 tests from WeightedHistogramModuleTest (17 ms total) 51: 51: [----------] 3 tests from BinAverageModuleTest 51: [ RUN ] BinAverageModuleTest.ComputesCorrectly 51: [ OK ] BinAverageModuleTest.ComputesCorrectly (1 ms) 51: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 51: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (1 ms) 51: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 51: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (1 ms) 51: [----------] 3 tests from BinAverageModuleTest (3 ms total) 51: 51: [----------] 4 tests from AbstractAverageHistogramTest 51: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 51: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (1 ms) 51: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 51: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (1 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (9 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (1 ms) 51: [----------] 4 tests from AbstractAverageHistogramTest (13 ms total) 51: 51: [----------] 3 tests from LifetimeModuleTest 51: [ RUN ] LifetimeModuleTest.BasicTest 51: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 51: [ RUN ] LifetimeModuleTest.CumulativeTest 51: [ OK ] LifetimeModuleTest.CumulativeTest (5 ms) 51: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 51: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 51: [----------] 3 tests from LifetimeModuleTest (7 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 69 tests from 14 test suites ran. (119 ms total) 51: [ PASSED ] 69 tests. 51/81 Test #51: AnalysisDataUnitTests .......................... Passed 0.18 sec test 52 Start 52: CoordinateIOTests 52: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 52: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/coordinateio/tests 52: Test timeout computed to be: 30 52: [==========] Running 64 tests from 19 test suites. 52: [----------] Global test environment set-up. 52: [----------] 1 test from OutputSelectorDeathTest 52: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (29 ms) 52: [----------] 1 test from OutputSelectorDeathTest (29 ms total) 52: 52: [----------] 5 tests from TrajectoryFrameWriterTest 52: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (8 ms) 52: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (9 ms) 52: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (5 ms) 52: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (10 ms) 52: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 52: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 52: [----------] 5 tests from TrajectoryFrameWriterTest (35 ms total) 52: 52: [----------] 5 tests from OutputAdapterContainer 52: [ RUN ] OutputAdapterContainer.MakeEmpty 52: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 52: [ RUN ] OutputAdapterContainer.AddAdapter 52: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 52: [ RUN ] OutputAdapterContainer.RejectBadAdapter 52: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 52: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 52: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 52: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 52: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 52: [----------] 5 tests from OutputAdapterContainer (0 ms total) 52: 52: [----------] 5 tests from FlagTest 52: [ RUN ] FlagTest.CanSetSimpleFlag 52: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 52: [ RUN ] FlagTest.CanAddNewBox 52: [ OK ] FlagTest.CanAddNewBox (0 ms) 52: [ RUN ] FlagTest.SetsImplicitPrecisionChange 52: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 52: [ RUN ] FlagTest.SetsImplicitStartTimeChange 52: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 52: [ RUN ] FlagTest.SetsImplicitTimeStepChange 52: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 52: [----------] 5 tests from FlagTest (0 ms total) 52: 52: [----------] 5 tests from SetAtomsTest 52: [ RUN ] SetAtomsTest.RemovesExistingAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.RemovesExistingAtoms (7 ms) 52: [ RUN ] SetAtomsTest.AddsNewAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.AddsNewAtoms (5 ms) 52: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (5 ms) 52: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (5 ms) 52: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (5 ms) 52: [----------] 5 tests from SetAtomsTest (29 ms total) 52: 52: [----------] 2 tests from SetBothTimeTest 52: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 52: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 52: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 52: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 52: [----------] 2 tests from SetBothTimeTest (0 ms total) 52: 52: [----------] 2 tests from SetStartTimeTest 52: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 52: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 52: [ RUN ] SetStartTimeTest.WorksWithZeroStart 52: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 52: [----------] 2 tests from SetStartTimeTest (0 ms total) 52: 52: [----------] 1 test from SetTimeStepTest 52: [ RUN ] SetTimeStepTest.SetTimeStepWorks 52: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 52: [----------] 1 test from SetTimeStepTest (0 ms total) 52: 52: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (6 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (5 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (5 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (5 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (5 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (5 ms) 52: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (34 ms total) 52: 52: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 52: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (7 ms) 52: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (6 ms) 52: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (4 ms) 52: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (19 ms total) 52: 52: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 52: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 52: 52: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (10 ms) 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (10 ms) 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (9 ms) 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (10 ms) 52: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (41 ms total) 52: 52: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 52: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (4 ms) 52: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (5 ms) 52: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (4 ms) 52: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (14 ms total) 52: 52: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 52: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 52: 52: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 52: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (4 ms) 52: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (4 ms) 52: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (9 ms total) 52: 52: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 52: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 52: 52: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 52: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (5 ms) 52: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (4 ms) 52: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (10 ms total) 52: 52: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 52: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 52: 52: [----------] 4 tests from ModuleSupported/NoOptionalOutput 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (5 ms) 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (11 ms) 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (4 ms) 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (4 ms) 52: [----------] 4 tests from ModuleSupported/NoOptionalOutput (25 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 64 tests from 19 test suites ran. (252 ms total) 52: [ PASSED ] 64 tests. 52/81 Test #52: CoordinateIOTests .............................. Passed 0.31 sec test 53 Start 53: TrajectoryAnalysisUnitTests 53: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests 53: Test timeout computed to be: 1920 53: [==========] Running 96 tests from 17 test suites. 53: [----------] Global test environment set-up. 53: [----------] 11 tests from AngleModuleTest 53: [ RUN ] AngleModuleTest.ComputesSimpleAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesSimpleAngles (8 ms) 53: [ RUN ] AngleModuleTest.ComputesDihedrals 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesDihedrals (12 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorPairAngles (3 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (11 ms) 53: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (8 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (11 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 53: Reading frames from gro file 'Test system for different angles', 33 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (4 ms) 53: [ RUN ] AngleModuleTest.ComputesMultipleAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesMultipleAngles (12 ms) 53: [ RUN ] AngleModuleTest.HandlesDynamicSelections 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.HandlesDynamicSelections (11 ms) 53: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (3 ms) 53: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (12 ms) 53: [----------] 11 tests from AngleModuleTest (101 ms total) 53: 53: [----------] 5 tests from ClustsizeTest 53: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 53: There is one group in the index 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 24 53: cmid: 2, cmax: 4, max_size: 6 53: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 53: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (6 ms) 53: [ RUN ] ClustsizeTest.NoMolShortCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 53: There is one group in the index 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 24 53: cmid: 1, cmax: 6, max_size: 6 53: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 53: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (1 ms) 53: [ RUN ] ClustsizeTest.MolDefaultCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 8 53: cmid: 2, cmax: 4, max_size: 2 53: 50%100%cmid: 2, cmax: 6, max_size: 2 53: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (10 ms) 53: [ RUN ] ClustsizeTest.MolShortCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 8 53: cmid: 1, cmax: 6, max_size: 2 53: 50%100%cmid: 2, cmax: 6, max_size: 2 53: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (2 ms) 53: [ RUN ] ClustsizeTest.MolCSize 53: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 8 53: cmid: 2, cmax: 4, max_size: 2 53: 50%100%cmid: 2, cmax: 6, max_size: 2 53: 50%100%[ OK ] ClustsizeTest.MolCSize (2 ms) 53: [----------] 5 tests from ClustsizeTest (23 ms total) 53: 53: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 53: Reading frames from gro file 'Test system', 8 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (11 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 53: Reading frames from gro file 'Test system', 8 atoms. 53: Reading frame 0 time 0.000 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (7 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 53: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (21 ms total) 53: 53: [----------] 4 tests from ConvertTrjModuleTest 53: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (38 ms) 53: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (25 ms) 53: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (10 ms) 53: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (2 ms) 53: [----------] 4 tests from ConvertTrjModuleTest (77 ms total) 53: 53: [----------] 6 tests from DistanceModuleTest 53: [ RUN ] DistanceModuleTest.ComputesDistances 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: atomname S1 S2: 53: Number of samples: 5 53: Average distance: 1.43246 nm 53: Standard deviation: 0.96700 nm 53: [ OK ] DistanceModuleTest.ComputesDistances (12 ms) 53: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: atomname S1 S2: 53: Number of samples: 5 53: Average distance: 1.43246 nm 53: Standard deviation: 0.96700 nm 53: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 53: Number of samples: 4 53: Average distance: 1.81066 nm 53: Standard deviation: 0.79289 nm 53: [ OK ] DistanceModuleTest.ComputesMultipleDistances (5 ms) 53: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: atomname S1 S2 and res_cog x < 2.8: 53: Number of samples: 3 53: Average distance: 1.72076 nm 53: Standard deviation: 1.24839 nm 53: [ OK ] DistanceModuleTest.HandlesDynamicSelections (13 ms) 53: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: Contacts: 53: Number of samples: 2 53: Average distance: 1.00000 nm 53: Standard deviation: 0.00000 nm 53: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (12 ms) 53: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: SuccessiveContacts: 53: Number of samples: 2 53: Average distance: 1.00000 nm 53: Standard deviation: 0.00000 nm 53: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (13 ms) 53: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: ManyContacts: 53: Number of samples: 10 53: Average distance: 1.82913 nm 53: Standard deviation: 0.78478 nm 53: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (17 ms) 53: [----------] 6 tests from DistanceModuleTest (77 ms total) 53: 53: [----------] 2 tests from ExtractClusterModuleTest 53: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 53: trr version: GMX_trn_file (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 53: Analyzed 26 frames, last time 0.050 53: There are 8 clusters containing 26 structures, highest framenr is 25 53: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (3 ms) 53: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 53: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 53: Analyzed 26 frames, last time 0.050 53: There are 8 clusters containing 26 structures, highest framenr is 25 53: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (6 ms) 53: [----------] 2 tests from ExtractClusterModuleTest (10 ms total) 53: 53: [----------] 2 tests from FreeVolumeModuleTest 53: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for 40 particles. These were set to zero. 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: cutoff = 0.18 nm 53: probe_radius = 0 nm 53: seed = 13 53: ninsert = 1000 probes per nm^3 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 53: van der Spoel and Luciano T. Costa 53: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 53: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 53: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Free volume 38.02 +/- 0.00 % 53: Total volume 68.92 +/- 0.00 nm^3 53: Number of molecules 340 total mass 63491.38 Dalton 53: Average molar mass: 186.74 Dalton 53: Density rho: 1529.71 +/- 0.00 nm^3 53: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 53: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 53: Fractional free volume 0.194 +/- 0.000 53: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (118 ms) 53: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: cutoff = 0.18 nm 53: probe_radius = 0 nm 53: seed = 17 53: ninsert = 1000 probes per nm^3 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 53: van der Spoel and Luciano T. Costa 53: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 53: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 53: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Free volume 38.48 +/- 0.00 % 53: Total volume 68.92 +/- 0.00 nm^3 53: Number of molecules 340 total mass 63491.38 Dalton 53: Average molar mass: 186.74 Dalton 53: Density rho: 1529.71 +/- 0.00 nm^3 53: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 53: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 53: Fractional free volume 0.200 +/- 0.000 53: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (127 ms) 53: [----------] 2 tests from FreeVolumeModuleTest (246 ms total) 53: 53: [----------] 11 tests from MsdModuleTest 53: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.threeDimensionalDiffusion (3 ms) 53: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.twoDimensionalDiffusion (4 ms) 53: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.oneDimensionalDiffusion (3 ms) 53: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (3 ms) 53: [ RUN ] MsdModuleTest.multipleGroupsWork 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -336593069 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.multipleGroupsWork (39 ms) 53: [ RUN ] MsdModuleTest.trestartLessThanDt 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to 1607720959 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.trestartLessThanDt (37 ms) 53: [ RUN ] MsdModuleTest.trestartGreaterThanDt 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -1628811947 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.trestartGreaterThanDt (36 ms) 53: [ RUN ] MsdModuleTest.molTest 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -80250884 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.molTest (35 ms) 53: [ RUN ] MsdModuleTest.beginFit 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -18159633 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.beginFit (35 ms) 53: [ RUN ] MsdModuleTest.endFit 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -1076922951 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.endFit (35 ms) 53: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: NOTE: You provided an index file 53: /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 53: (with -n), but it was not used by any selection. 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -545785861 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (37 ms) 53: [----------] 11 tests from MsdModuleTest (274 ms total) 53: 53: [----------] 9 tests from PairDistanceModuleTest 53: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesAllDistances (4 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (4 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (3 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (3 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (3 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (3 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (3 ms) 53: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (3 ms) 53: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (3 ms) 53: [----------] 9 tests from PairDistanceModuleTest (34 ms total) 53: 53: [----------] 5 tests from RdfModuleTest 53: [ RUN ] RdfModuleTest.BasicTest 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.BasicTest (31 ms) 53: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 53: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (24 ms) 53: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (37 ms) 53: [ RUN ] RdfModuleTest.CalculatesSurf 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.CalculatesSurf (19 ms) 53: [ RUN ] RdfModuleTest.CalculatesXY 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.CalculatesXY (39 ms) 53: [----------] 5 tests from RdfModuleTest (153 ms total) 53: 53: [----------] 5 tests from SasaModuleTest 53: [ RUN ] SasaModuleTest.BasicTest 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.BasicTest (19 ms) 53: [ RUN ] SasaModuleTest.HandlesSelectedResidues 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.HandlesSelectedResidues (14 ms) 53: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (8 ms) 53: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (12 ms) 53: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (14 ms) 53: [----------] 5 tests from SasaModuleTest (72 ms total) 53: 53: [----------] 8 tests from SelectModuleTest 53: [ RUN ] SelectModuleTest.BasicTest 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.BasicTest (8 ms) 53: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (4 ms) 53: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (4 ms) 53: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (5 ms) 53: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (4 ms) 53: [ RUN ] SelectModuleTest.NormalizesSizes 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.NormalizesSizes (3 ms) 53: [ RUN ] SelectModuleTest.WritesResidueNumbers 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.WritesResidueNumbers (3 ms) 53: [ RUN ] SelectModuleTest.WritesResidueIndices 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.WritesResidueIndices (4 ms) 53: [----------] 8 tests from SelectModuleTest (40 ms total) 53: 53: [----------] 10 tests from SurfaceAreaTest 53: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 53: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 53: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 53: [ OK ] SurfaceAreaTest.ComputesTwoPoints (1 ms) 53: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 53: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (1 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints12 53: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints32 53: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints42 53: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints122 53: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms) 53: [ RUN ] SurfaceAreaTest.Computes100Points 53: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (3 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (4 ms) 53: [----------] 10 tests from SurfaceAreaTest (14 ms total) 53: 53: [----------] 4 tests from TopologyInformation 53: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 53: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 53: [ RUN ] TopologyInformation.WorksWithGroFile 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TopologyInformation.WorksWithGroFile (4 ms) 53: [ RUN ] TopologyInformation.WorksWithPdbFile 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TopologyInformation.WorksWithPdbFile (4 ms) 53: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file lysozyme.top, line 1465]: 53: System has non-zero total charge: 2.000000 53: Total charge should normally be an integer. See 53: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 53: for discussion on how close it should be to an integer. 53: 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 465.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 53: NVE simulation with an initial temperature of zero: will use a Verlet 53: buffer of 10%. Check your energy drift! 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 53: Setting the LD random seed to -570949765 53: 53: Generated 330891 of the 330891 non-bonded parameter combinations 53: 53: Generated 330891 of the 330891 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 53: Analysing residue names: 53: There are: 10 Protein residues 53: Analysing Protein... 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (616 ms) 53: [----------] 4 tests from TopologyInformation (626 ms total) 53: 53: [----------] 4 tests from TrajectoryModuleTest 53: [ RUN ] TrajectoryModuleTest.BasicTest 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.BasicTest (4 ms) 53: [ RUN ] TrajectoryModuleTest.PlotsXOnly 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.PlotsXOnly (4 ms) 53: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (4 ms) 53: [ RUN ] TrajectoryModuleTest.HandlesNoForces 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.HandlesNoForces (4 ms) 53: [----------] 4 tests from TrajectoryModuleTest (17 ms total) 53: 53: [----------] 5 tests from UnionFinderTest 53: [ RUN ] UnionFinderTest.WorksEmpty 53: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 53: [ RUN ] UnionFinderTest.BasicMerges 53: [ OK ] UnionFinderTest.BasicMerges (0 ms) 53: [ RUN ] UnionFinderTest.LargerMerges 53: [ OK ] UnionFinderTest.LargerMerges (0 ms) 53: [ RUN ] UnionFinderTest.LongRightMerge 53: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 53: [ RUN ] UnionFinderTest.LongLeftMerge 53: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 53: [----------] 5 tests from UnionFinderTest (0 ms total) 53: 53: [----------] 1 test from MappedUnionFinderTest 53: [ RUN ] MappedUnionFinderTest.BasicMerges 53: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 53: [----------] 1 test from MappedUnionFinderTest (0 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 96 tests from 17 test suites ran. (1791 ms total) 53: [ PASSED ] 96 tests. 53/81 Test #53: TrajectoryAnalysisUnitTests .................... Passed 1.87 sec test 54 Start 54: EnergyAnalysisUnitTests 54: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/energyanalysis/tests 54: Test timeout computed to be: 30 54: [==========] Running 7 tests from 4 test suites. 54: [----------] Global test environment set-up. 54: [----------] 1 test from DhdlTest 54: [ RUN ] DhdlTest.ExtractDhdl 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 54: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 54: Note: file tpx version 110, software tpx version 127 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 54: 54: 54: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 54: [ OK ] DhdlTest.ExtractDhdl (29 ms) 54: [----------] 1 test from DhdlTest (30 ms total) 54: 54: [----------] 1 test from OriresTest 54: [ RUN ] OriresTest.ExtractOrires 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 54: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 54: Note: file tpx version 111, software tpx version 127 54: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 54: End your selection with 0 54: Selecting all 7 orientation restraints 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 54: [ OK ] OriresTest.ExtractOrires (33 ms) 54: [----------] 1 test from OriresTest (33 ms total) 54: 54: [----------] 3 tests from EnergyTest 54: [ RUN ] EnergyTest.ExtractEnergy 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: 54: Select the terms you want from the following list by 54: selecting either (part of) the name or the number or a combination. 54: End your selection with an empty line or a zero. 54: ------------------------------------------------------------------- 54: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 54: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 54: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 54: 13 Box-Z 14 Volume 15 Density 16 pV 54: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 54: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 54: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 54: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 54: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 54: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 54: 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 54: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 54: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 54: [ OK ] EnergyTest.ExtractEnergy (7 ms) 54: [ RUN ] EnergyTest.ExtractEnergyByNumber 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: 54: Select the terms you want from the following list by 54: selecting either (part of) the name or the number or a combination. 54: End your selection with an empty line or a zero. 54: ------------------------------------------------------------------- 54: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 54: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 54: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 54: 13 Box-Z 14 Volume 15 Density 16 pV 54: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 54: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 54: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 54: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 54: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 54: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 54: 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 54: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 54: Pres. DC -268.49 3 8.52175 13.2804 (bar) 54: [ OK ] EnergyTest.ExtractEnergyByNumber (7 ms) 54: [ RUN ] EnergyTest.ExtractEnergyMixed 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: 54: Select the terms you want from the following list by 54: selecting either (part of) the name or the number or a combination. 54: End your selection with an empty line or a zero. 54: ------------------------------------------------------------------- 54: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 54: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 54: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 54: 13 Box-Z 14 Volume 15 Density 16 pV 54: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 54: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 54: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 54: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 54: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 54: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 54: 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 54: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 54: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 54: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 54: [ OK ] EnergyTest.ExtractEnergyMixed (11 ms) 54: [----------] 3 tests from EnergyTest (27 ms total) 54: 54: [----------] 2 tests from ViscosityTest 54: [ RUN ] ViscosityTest.EinsteinViscosity 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Pres-XX 20.2092 65 717.193 185.978 (bar) 54: Pres-XY -47.7351 39 372.522 207.456 (bar) 54: Pres-XZ 11.477 31 379.79 6.80818 (bar) 54: Pres-YX -47.7106 39 372.525 207.5 (bar) 54: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 54: Pres-YZ -41.3534 45 401.216 114.663 (bar) 54: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 54: Pres-ZY -41.3119 45 401.196 114.743 (bar) 54: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 54: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 54: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 54: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 54: [ OK ] ViscosityTest.EinsteinViscosity (282 ms) 54: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Pres-XX 20.2092 65 717.193 185.978 (bar) 54: Pres-XY -47.7351 39 372.522 207.456 (bar) 54: Pres-XZ 11.477 31 379.79 6.80818 (bar) 54: Pres-YX -47.7106 39 372.525 207.5 (bar) 54: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 54: Pres-YZ -41.3534 45 401.216 114.663 (bar) 54: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 54: Pres-ZY -41.3119 45 401.196 114.743 (bar) 54: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 54: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 54: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 54: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 54: [ OK ] ViscosityTest.EinsteinViscosityIntegral (244 ms) 54: [----------] 2 tests from ViscosityTest (526 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 7 tests from 4 test suites ran. (618 ms total) 54: [ PASSED ] 7 tests. 54/81 Test #54: EnergyAnalysisUnitTests ........................ Passed 0.67 sec test 55 Start 55: ToolUnitTests 55: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests 55: Test timeout computed to be: 1920 55: [==========] Running 54 tests from 6 test suites. 55: [----------] Global test environment set-up. 55: [----------] 2 tests from DumpTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Setting the LD random seed to -59335184 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: [ RUN ] DumpTest.WorksWithTpr 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 55: inputrec: 55: integrator = md 55: tinit = 0 55: dt = 0.001 55: nsteps = 0 55: init-step = 0 55: simulation-part = 1 55: mts = false 55: comm-mode = Linear 55: nstcomm = 100 55: bd-fric = 0 55: ld-seed = -59335184 55: emtol = 10 55: emstep = 0.01 55: niter = 20 55: fcstep = 0 55: nstcgsteep = 1000 55: nbfgscorr = 10 55: rtpi = 0.05 55: nstxout = 0 55: nstvout = 0 55: nstfout = 0 55: nstlog = 1000 55: nstcalcenergy = 100 55: nstenergy = 1000 55: nstxout-compressed = 0 55: compressed-x-precision = 1000 55: cutoff-scheme = Verlet 55: nstlist = 10 55: pbc = xyz 55: periodic-molecules = false 55: verlet-buffer-tolerance = -1 55: rlist = 1.1 55: coulombtype = Cut-off 55: coulomb-modifier = Potential-shift 55: rcoulomb-switch = 0 55: rcoulomb = 1 55: epsilon-r = 1 55: epsilon-rf = inf 55: vdw-type = Cut-off 55: vdw-modifier = Potential-shift 55: rvdw-switch = 0 55: rvdw = 1 55: DispCorr = No 55: table-extension = 1 55: fourierspacing = 0.12 55: fourier-nx = 0 55: fourier-ny = 0 55: fourier-nz = 0 55: pme-order = 4 55: ewald-rtol = 1e-05 55: ewald-rtol-lj = 0.001 55: lj-pme-comb-rule = Geometric 55: ewald-geometry = 3d 55: epsilon-surface = 0 55: tcoupl = No 55: nsttcouple = -1 55: nh-chain-length = 0 55: print-nose-hoover-chain-variables = false 55: pcoupl = No 55: pcoupltype = Isotropic 55: nstpcouple = -1 55: tau-p = 1 55: compressibility (3x3): 55: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: ref-p (3x3): 55: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: refcoord-scaling = No 55: posres-com (3): 55: posres-com[0]= 0.00000e+00 55: posres-com[1]= 0.00000e+00 55: posres-com[2]= 0.00000e+00 55: posres-comB (3): 55: posres-comB[0]= 0.00000e+00 55: posres-comB[1]= 0.00000e+00 55: posres-comB[2]= 0.00000e+00 55: QMMM = false 55: qm-opts: 55: ngQM = 0 55: constraint-algorithm = Lincs 55: continuation = false 55: Shake-SOR = false 55: shake-tol = 0.0001 55: lincs-order = 4 55: lincs-iter = 1 55: lincs-warnangle = 30 55: nwall = 0 55: wall-type = 9-3 55: wall-r-linpot = -1 55: wall-atomtype[0] = -1 55: wall-atomtype[1] = -1 55: wall-density[0] = 0 55: wall-density[1] = 0 55: wall-ewald-zfac = 3 55: pull = false 55: awh = false 55: rotation = false 55: interactiveMD = false 55: disre = No 55: disre-weighting = Conservative 55: disre-mixed = false 55: dr-fc = 1000 55: dr-tau = 0 55: nstdisreout = 100 55: orire-fc = 0 55: orire-tau = 0 55: nstorireout = 100 55: free-energy = no 55: cos-acceleration = 0 55: deform (3x3): 55: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: simulated-tempering = false 55: swapcoords = no 55: userint1 = 0 55: userint2 = 0 55: userint3 = 0 55: userint4 = 0 55: userreal1 = 0 55: userreal2 = 0 55: userreal3 = 0 55: userreal4 = 0 55: applied-forces: 55: electric-field: 55: x: 55: E0 = 0 55: omega = 0 55: t0 = 0 55: sigma = 0 55: y: 55: E0 = 0 55: omega = 0 55: t0 = 0 55: sigma = 0 55: z: 55: E0 = 0 55: omega = 0 55: t0 = 0 55: sigma = 0 55: density-guided-simulation: 55: active = false 55: group = protein 55: similarity-measure = inner-product 55: atom-spreading-weight = unity 55: force-constant = 1e+09 55: gaussian-transform-spreading-width = 0.2 55: gaussian-transform-spreading-range-in-multiples-of-width = 4 55: reference-density-filename = reference.mrc 55: nst = 1 55: normalize-densities = true 55: adaptive-force-scaling = false 55: adaptive-force-scaling-time-constant = 4 55: shift-vector = 55: transformation-matrix = 55: qmmm-cp2k: 55: active = false 55: qmgroup = System 55: qmmethod = PBE 55: qmfilenames = 55: qmcharge = 0 55: qmmultiplicity = 1 55: grpopts: 55: nrdf: 465 55: ref-t: 0 55: tau-t: 0 55: annealing: No 55: annealing-npoints: 0 55: acc: 0 0 0 55: nfreeze: N N N 55: energygrp-flags[ 0]: 0 55: header: 55: bIr = present 55: bBox = present 55: bTop = present 55: bX = present 55: bV = present 55: bF = not present 55: natoms = 156 55: lambda = 0.000000e+00 55: buffer size = 70358 55: topology: 55: name="First 10 residues from 1AKI" 55: #atoms = 156 55: #molblock = 1 55: molblock (0): 55: moltype = 0 "Protein_chain_B" 55: #molecules = 1 55: #posres_xA = 0 55: #posres_xB = 0 55: bIntermolecularInteractions = false 55: ffparams: 55: atnr=10 55: ntypes=212 55: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 55: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 55: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 55: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 55: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 55: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06 55: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07 55: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07 55: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05 55: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 55: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06 55: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 55: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06 55: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06 55: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06 55: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07 55: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07 55: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05 55: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 55: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07 55: 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functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06 55: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05 55: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07 55: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07 55: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05 55: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 55: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 55: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 55: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 55: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 55: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 55: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 55: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 55: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 55: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 55: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 55: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 55: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 55: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 55: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 55: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 55: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 55: functype[117]=ANGLES, thA= 1.11200e+02, 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1.18400e+02, ctB= 3.17984e+02 55: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 55: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 55: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 55: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 55: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 55: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 55: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 55: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 55: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 55: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 55: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 55: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 55: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2 55: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2 55: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2 55: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 55: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 55: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 55: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 55: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 55: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 55: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 55: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 55: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 55: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 55: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 55: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 55: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 55: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 55: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 55: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 55: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 55: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 55: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 55: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 55: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 55: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 55: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 55: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 55: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 55: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 55: reppow = 12 55: fudgeQQ = 0.5 55: cmap 55: atomtypes: 55: atomtype[ 0]={atomnumber= 7} 55: atomtype[ 1]={atomnumber= 1} 55: atomtype[ 2]={atomnumber= 6} 55: atomtype[ 3]={atomnumber= 1} 55: atomtype[ 4]={atomnumber= 6} 55: atomtype[ 5]={atomnumber= 8} 55: atomtype[ 6]={atomnumber= 6} 55: atomtype[ 7]={atomnumber= 1} 55: atomtype[ 8]={atomnumber= 6} 55: atomtype[ 9]={atomnumber= 16} 55: moltype (0): 55: name="Protein_chain_B" 55: atoms: 55: atom (156): 55: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 55: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 55: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 55: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 55: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 55: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 55: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 55: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 55: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 55: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 55: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 55: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 55: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 55: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 55: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 55: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 55: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 55: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 55: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 55: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 55: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 55: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 55: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 55: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 55: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 55: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 55: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 55: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 55: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 55: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 55: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 55: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 55: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 55: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 55: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 55: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 55: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 55: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 55: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 55: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 55: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 55: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 55: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 55: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 55: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 55: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 55: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 55: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 55: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 55: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 55: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 55: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 55: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 55: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 55: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 55: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 55: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 55: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 55: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 55: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 55: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 55: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 55: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 55: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 55: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 55: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 55: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 55: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 55: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 55: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 55: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 55: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 55: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 55: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 55: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 55: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 55: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 55: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 55: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 55: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 55: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 55: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 55: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 55: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 55: atom (156): 55: atom[0]={name="N"} 55: atom[1]={name="H1"} 55: atom[2]={name="H2"} 55: atom[3]={name="H3"} 55: atom[4]={name="CA"} 55: atom[5]={name="HA"} 55: atom[6]={name="CB"} 55: atom[7]={name="HB1"} 55: atom[8]={name="HB2"} 55: atom[9]={name="CG"} 55: atom[10]={name="HG1"} 55: atom[11]={name="HG2"} 55: atom[12]={name="CD"} 55: atom[13]={name="HD1"} 55: atom[14]={name="HD2"} 55: atom[15]={name="CE"} 55: atom[16]={name="HE1"} 55: atom[17]={name="HE2"} 55: atom[18]={name="NZ"} 55: atom[19]={name="HZ1"} 55: atom[20]={name="HZ2"} 55: atom[21]={name="HZ3"} 55: atom[22]={name="C"} 55: atom[23]={name="O"} 55: atom[24]={name="N"} 55: atom[25]={name="H"} 55: atom[26]={name="CA"} 55: atom[27]={name="HA"} 55: atom[28]={name="CB"} 55: atom[29]={name="HB"} 55: atom[30]={name="CG1"} 55: atom[31]={name="HG11"} 55: atom[32]={name="HG12"} 55: atom[33]={name="HG13"} 55: atom[34]={name="CG2"} 55: atom[35]={name="HG21"} 55: atom[36]={name="HG22"} 55: atom[37]={name="HG23"} 55: atom[38]={name="C"} 55: atom[39]={name="O"} 55: atom[40]={name="N"} 55: atom[41]={name="H"} 55: atom[42]={name="CA"} 55: atom[43]={name="HA"} 55: atom[44]={name="CB"} 55: atom[45]={name="HB1"} 55: atom[46]={name="HB2"} 55: atom[47]={name="CG"} 55: atom[48]={name="CD1"} 55: atom[49]={name="HD1"} 55: atom[50]={name="CD2"} 55: atom[51]={name="HD2"} 55: atom[52]={name="CE1"} 55: atom[53]={name="HE1"} 55: atom[54]={name="CE2"} 55: atom[55]={name="HE2"} 55: atom[56]={name="CZ"} 55: atom[57]={name="HZ"} 55: atom[58]={name="C"} 55: atom[59]={name="O"} 55: atom[60]={name="N"} 55: atom[61]={name="H"} 55: atom[62]={name="CA"} 55: atom[63]={name="HA1"} 55: atom[64]={name="HA2"} 55: atom[65]={name="C"} 55: atom[66]={name="O"} 55: atom[67]={name="N"} 55: atom[68]={name="H"} 55: atom[69]={name="CA"} 55: atom[70]={name="HA"} 55: atom[71]={name="CB"} 55: atom[72]={name="HB1"} 55: atom[73]={name="HB2"} 55: atom[74]={name="CG"} 55: atom[75]={name="HG1"} 55: atom[76]={name="HG2"} 55: atom[77]={name="CD"} 55: atom[78]={name="HD1"} 55: atom[79]={name="HD2"} 55: atom[80]={name="NE"} 55: atom[81]={name="HE"} 55: atom[82]={name="CZ"} 55: atom[83]={name="NH1"} 55: atom[84]={name="HH11"} 55: atom[85]={name="HH12"} 55: atom[86]={name="NH2"} 55: atom[87]={name="HH21"} 55: atom[88]={name="HH22"} 55: atom[89]={name="C"} 55: atom[90]={name="O"} 55: atom[91]={name="N"} 55: atom[92]={name="H"} 55: atom[93]={name="CA"} 55: atom[94]={name="HA"} 55: atom[95]={name="CB"} 55: atom[96]={name="HB1"} 55: atom[97]={name="HB2"} 55: atom[98]={name="SG"} 55: atom[99]={name="HG"} 55: atom[100]={name="C"} 55: atom[101]={name="O"} 55: atom[102]={name="N"} 55: atom[103]={name="H"} 55: atom[104]={name="CA"} 55: atom[105]={name="HA"} 55: atom[106]={name="CB"} 55: atom[107]={name="HB1"} 55: atom[108]={name="HB2"} 55: atom[109]={name="CG"} 55: atom[110]={name="HG1"} 55: atom[111]={name="HG2"} 55: atom[112]={name="CD"} 55: atom[113]={name="OE1"} 55: atom[114]={name="OE2"} 55: atom[115]={name="C"} 55: atom[116]={name="O"} 55: atom[117]={name="N"} 55: atom[118]={name="H"} 55: atom[119]={name="CA"} 55: atom[120]={name="HA"} 55: atom[121]={name="CB"} 55: atom[122]={name="HB1"} 55: atom[123]={name="HB2"} 55: atom[124]={name="CG"} 55: atom[125]={name="HG"} 55: atom[126]={name="CD1"} 55: atom[127]={name="HD11"} 55: atom[128]={name="HD12"} 55: atom[129]={name="HD13"} 55: atom[130]={name="CD2"} 55: atom[131]={name="HD21"} 55: atom[132]={name="HD22"} 55: atom[133]={name="HD23"} 55: atom[134]={name="C"} 55: atom[135]={name="O"} 55: atom[136]={name="N"} 55: atom[137]={name="H"} 55: atom[138]={name="CA"} 55: atom[139]={name="HA"} 55: atom[140]={name="CB"} 55: atom[141]={name="HB1"} 55: atom[142]={name="HB2"} 55: atom[143]={name="HB3"} 55: atom[144]={name="C"} 55: atom[145]={name="O"} 55: atom[146]={name="N"} 55: atom[147]={name="H"} 55: atom[148]={name="CA"} 55: atom[149]={name="HA"} 55: atom[150]={name="CB"} 55: atom[151]={name="HB1"} 55: atom[152]={name="HB2"} 55: atom[153]={name="HB3"} 55: atom[154]={name="C"} 55: atom[155]={name="O"} 55: type (156): 55: type[0]={name="opls_287",nameB="opls_287"} 55: type[1]={name="opls_290",nameB="opls_290"} 55: type[2]={name="opls_290",nameB="opls_290"} 55: type[3]={name="opls_290",nameB="opls_290"} 55: type[4]={name="opls_293B",nameB="opls_293B"} 55: type[5]={name="opls_140",nameB="opls_140"} 55: type[6]={name="opls_136",nameB="opls_136"} 55: type[7]={name="opls_140",nameB="opls_140"} 55: type[8]={name="opls_140",nameB="opls_140"} 55: type[9]={name="opls_136",nameB="opls_136"} 55: type[10]={name="opls_140",nameB="opls_140"} 55: type[11]={name="opls_140",nameB="opls_140"} 55: type[12]={name="opls_136",nameB="opls_136"} 55: type[13]={name="opls_140",nameB="opls_140"} 55: type[14]={name="opls_140",nameB="opls_140"} 55: type[15]={name="opls_292",nameB="opls_292"} 55: type[16]={name="opls_140",nameB="opls_140"} 55: type[17]={name="opls_140",nameB="opls_140"} 55: type[18]={name="opls_287",nameB="opls_287"} 55: type[19]={name="opls_290",nameB="opls_290"} 55: type[20]={name="opls_290",nameB="opls_290"} 55: type[21]={name="opls_290",nameB="opls_290"} 55: type[22]={name="opls_235",nameB="opls_235"} 55: type[23]={name="opls_236",nameB="opls_236"} 55: type[24]={name="opls_238",nameB="opls_238"} 55: type[25]={name="opls_241",nameB="opls_241"} 55: type[26]={name="opls_224B",nameB="opls_224B"} 55: type[27]={name="opls_140",nameB="opls_140"} 55: type[28]={name="opls_137",nameB="opls_137"} 55: type[29]={name="opls_140",nameB="opls_140"} 55: type[30]={name="opls_135",nameB="opls_135"} 55: type[31]={name="opls_140",nameB="opls_140"} 55: type[32]={name="opls_140",nameB="opls_140"} 55: type[33]={name="opls_140",nameB="opls_140"} 55: type[34]={name="opls_135",nameB="opls_135"} 55: type[35]={name="opls_140",nameB="opls_140"} 55: type[36]={name="opls_140",nameB="opls_140"} 55: type[37]={name="opls_140",nameB="opls_140"} 55: type[38]={name="opls_235",nameB="opls_235"} 55: type[39]={name="opls_236",nameB="opls_236"} 55: type[40]={name="opls_238",nameB="opls_238"} 55: type[41]={name="opls_241",nameB="opls_241"} 55: type[42]={name="opls_224B",nameB="opls_224B"} 55: type[43]={name="opls_140",nameB="opls_140"} 55: type[44]={name="opls_149",nameB="opls_149"} 55: type[45]={name="opls_140",nameB="opls_140"} 55: type[46]={name="opls_140",nameB="opls_140"} 55: type[47]={name="opls_145",nameB="opls_145"} 55: type[48]={name="opls_145",nameB="opls_145"} 55: type[49]={name="opls_146",nameB="opls_146"} 55: type[50]={name="opls_145",nameB="opls_145"} 55: type[51]={name="opls_146",nameB="opls_146"} 55: type[52]={name="opls_145",nameB="opls_145"} 55: type[53]={name="opls_146",nameB="opls_146"} 55: type[54]={name="opls_145",nameB="opls_145"} 55: type[55]={name="opls_146",nameB="opls_146"} 55: type[56]={name="opls_145",nameB="opls_145"} 55: type[57]={name="opls_146",nameB="opls_146"} 55: type[58]={name="opls_235",nameB="opls_235"} 55: type[59]={name="opls_236",nameB="opls_236"} 55: type[60]={name="opls_238",nameB="opls_238"} 55: type[61]={name="opls_241",nameB="opls_241"} 55: type[62]={name="opls_223B",nameB="opls_223B"} 55: type[63]={name="opls_140",nameB="opls_140"} 55: type[64]={name="opls_140",nameB="opls_140"} 55: type[65]={name="opls_235",nameB="opls_235"} 55: type[66]={name="opls_236",nameB="opls_236"} 55: type[67]={name="opls_238",nameB="opls_238"} 55: type[68]={name="opls_241",nameB="opls_241"} 55: type[69]={name="opls_224B",nameB="opls_224B"} 55: type[70]={name="opls_140",nameB="opls_140"} 55: type[71]={name="opls_136",nameB="opls_136"} 55: type[72]={name="opls_140",nameB="opls_140"} 55: type[73]={name="opls_140",nameB="opls_140"} 55: type[74]={name="opls_308",nameB="opls_308"} 55: type[75]={name="opls_140",nameB="opls_140"} 55: type[76]={name="opls_140",nameB="opls_140"} 55: type[77]={name="opls_307",nameB="opls_307"} 55: type[78]={name="opls_140",nameB="opls_140"} 55: type[79]={name="opls_140",nameB="opls_140"} 55: type[80]={name="opls_303",nameB="opls_303"} 55: type[81]={name="opls_304",nameB="opls_304"} 55: type[82]={name="opls_302",nameB="opls_302"} 55: type[83]={name="opls_300",nameB="opls_300"} 55: type[84]={name="opls_301",nameB="opls_301"} 55: type[85]={name="opls_301",nameB="opls_301"} 55: type[86]={name="opls_300",nameB="opls_300"} 55: type[87]={name="opls_301",nameB="opls_301"} 55: type[88]={name="opls_301",nameB="opls_301"} 55: type[89]={name="opls_235",nameB="opls_235"} 55: type[90]={name="opls_236",nameB="opls_236"} 55: type[91]={name="opls_238",nameB="opls_238"} 55: type[92]={name="opls_241",nameB="opls_241"} 55: type[93]={name="opls_224B",nameB="opls_224B"} 55: type[94]={name="opls_140",nameB="opls_140"} 55: type[95]={name="opls_206",nameB="opls_206"} 55: type[96]={name="opls_140",nameB="opls_140"} 55: type[97]={name="opls_140",nameB="opls_140"} 55: type[98]={name="opls_200",nameB="opls_200"} 55: type[99]={name="opls_204",nameB="opls_204"} 55: type[100]={name="opls_235",nameB="opls_235"} 55: type[101]={name="opls_236",nameB="opls_236"} 55: type[102]={name="opls_238",nameB="opls_238"} 55: type[103]={name="opls_241",nameB="opls_241"} 55: type[104]={name="opls_224B",nameB="opls_224B"} 55: type[105]={name="opls_140",nameB="opls_140"} 55: type[106]={name="opls_136",nameB="opls_136"} 55: type[107]={name="opls_140",nameB="opls_140"} 55: type[108]={name="opls_140",nameB="opls_140"} 55: type[109]={name="opls_274",nameB="opls_274"} 55: type[110]={name="opls_140",nameB="opls_140"} 55: type[111]={name="opls_140",nameB="opls_140"} 55: type[112]={name="opls_271",nameB="opls_271"} 55: type[113]={name="opls_272",nameB="opls_272"} 55: type[114]={name="opls_272",nameB="opls_272"} 55: type[115]={name="opls_235",nameB="opls_235"} 55: type[116]={name="opls_236",nameB="opls_236"} 55: type[117]={name="opls_238",nameB="opls_238"} 55: type[118]={name="opls_241",nameB="opls_241"} 55: type[119]={name="opls_224B",nameB="opls_224B"} 55: type[120]={name="opls_140",nameB="opls_140"} 55: type[121]={name="opls_136",nameB="opls_136"} 55: type[122]={name="opls_140",nameB="opls_140"} 55: type[123]={name="opls_140",nameB="opls_140"} 55: type[124]={name="opls_137",nameB="opls_137"} 55: type[125]={name="opls_140",nameB="opls_140"} 55: type[126]={name="opls_135",nameB="opls_135"} 55: type[127]={name="opls_140",nameB="opls_140"} 55: type[128]={name="opls_140",nameB="opls_140"} 55: type[129]={name="opls_140",nameB="opls_140"} 55: type[130]={name="opls_135",nameB="opls_135"} 55: type[131]={name="opls_140",nameB="opls_140"} 55: type[132]={name="opls_140",nameB="opls_140"} 55: type[133]={name="opls_140",nameB="opls_140"} 55: type[134]={name="opls_235",nameB="opls_235"} 55: type[135]={name="opls_236",nameB="opls_236"} 55: type[136]={name="opls_238",nameB="opls_238"} 55: type[137]={name="opls_241",nameB="opls_241"} 55: type[138]={name="opls_224B",nameB="opls_224B"} 55: type[139]={name="opls_140",nameB="opls_140"} 55: type[140]={name="opls_135",nameB="opls_135"} 55: type[141]={name="opls_140",nameB="opls_140"} 55: type[142]={name="opls_140",nameB="opls_140"} 55: type[143]={name="opls_140",nameB="opls_140"} 55: type[144]={name="opls_235",nameB="opls_235"} 55: type[145]={name="opls_236",nameB="opls_236"} 55: type[146]={name="opls_238",nameB="opls_238"} 55: type[147]={name="opls_241",nameB="opls_241"} 55: type[148]={name="opls_224B",nameB="opls_224B"} 55: type[149]={name="opls_140",nameB="opls_140"} 55: type[150]={name="opls_135",nameB="opls_135"} 55: type[151]={name="opls_140",nameB="opls_140"} 55: type[152]={name="opls_140",nameB="opls_140"} 55: type[153]={name="opls_140",nameB="opls_140"} 55: type[154]={name="opls_235",nameB="opls_235"} 55: type[155]={name="opls_236",nameB="opls_236"} 55: residue (10): 55: residue[0]={name="LYS", nr=1, ic=' '} 55: residue[1]={name="VAL", nr=2, ic=' '} 55: residue[2]={name="PHE", nr=3, ic=' '} 55: residue[3]={name="GLY", nr=4, ic=' '} 55: residue[4]={name="ARG", nr=5, ic=' '} 55: residue[5]={name="CYS", nr=6, ic=' '} 55: residue[6]={name="GLU", nr=7, ic=' '} 55: residue[7]={name="LEU", nr=8, ic=' '} 55: residue[8]={name="ALA", nr=9, ic=' '} 55: residue[9]={name="ALA", nr=10, ic=' '} 55: excls: 55: numLists=156 55: numElements=1828 55: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 55: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 55: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 55: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 55: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 55: 23, 24, 25, 26} 55: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 55: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 55: 14, 15, 22, 23, 24} 55: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 55: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 55: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 55: 16, 17, 18, 22} 55: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 55: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 55: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 55: 17, 18, 19, 20, 21} 55: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 55: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 55: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 55: 20, 21} 55: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 55: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 55: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 55: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 55: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 55: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 55: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 55: 26, 27, 28, 38} 55: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 55: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 55: 30, 34, 38, 39, 40} 55: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 55: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 55: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 55: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 55: 40} 55: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 55: 34, 35, 36, 37, 38, 39, 40} 55: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55: 36, 37, 38} 55: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55: 36, 37, 38} 55: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 55: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 55: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 55: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55: 36, 37, 38} 55: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 55: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 55: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 55: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 55: 40, 41, 42, 43, 44, 58} 55: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 55: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 55: 45, 46, 47, 58, 59, 60} 55: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 55: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 55: 48, 50, 58, 59, 60, 61, 62} 55: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 55: 60} 55: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55: 50, 51, 52, 54, 58, 59, 60} 55: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 55: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 55: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 55: 52, 53, 54, 55, 56, 58} 55: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55: 54, 56, 57} 55: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 55: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55: 55, 56, 57} 55: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 55: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 55: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 55: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 55: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 55: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 55: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 55: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 55: 60, 61, 62, 63, 64, 65} 55: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 55: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 55: 65, 66, 67} 55: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 55: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 55: 68, 69} 55: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 55: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 55: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 55: 70, 71, 89} 55: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 55: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 55: 72, 73, 74, 89, 90, 91} 55: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 55: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 55: 75, 76, 77, 89, 90, 91, 92, 93} 55: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 55: 91} 55: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 55: 77, 78, 79, 80, 89, 90, 91} 55: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 55: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 55: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 55: 79, 80, 81, 82, 89} 55: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 55: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 55: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 55: 81, 82, 83, 86} 55: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 55: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 55: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 55: 84, 85, 86, 87, 88} 55: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 55: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 55: 87, 88} 55: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 55: excls[84][num=6]={80, 82, 83, 84, 85, 86} 55: excls[85][num=6]={80, 82, 83, 84, 85, 86} 55: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 55: excls[87][num=6]={80, 82, 83, 86, 87, 88} 55: excls[88][num=6]={80, 82, 83, 86, 87, 88} 55: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 55: 91, 92, 93, 94, 95, 100} 55: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 55: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 55: 96, 97, 98, 100, 101, 102} 55: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 55: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 55: 99, 100, 101, 102, 103, 104} 55: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 55: 102} 55: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 55: 101, 102} 55: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 55: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 55: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 55: excls[99][num=6]={93, 95, 96, 97, 98, 99} 55: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 55: 102, 103, 104, 105, 106, 115} 55: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 55: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 55: 106, 107, 108, 109, 115, 116, 117} 55: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 55: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 55: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 55: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 55: 115, 116, 117} 55: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 55: 110, 111, 112, 113, 114, 115, 116, 117} 55: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 55: 112, 115} 55: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 55: 112, 115} 55: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 55: 112, 113, 114, 115} 55: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 55: 114} 55: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 55: 114} 55: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 55: 114} 55: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 55: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 55: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 55: 115, 116, 117, 118, 119, 120, 121, 134} 55: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 55: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 55: 120, 121, 122, 123, 124, 134, 135, 136} 55: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 55: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 55: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 55: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 55: 134, 135, 136} 55: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 55: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 55: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 55: 130, 134} 55: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 55: 130, 134} 55: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 55: 127, 128, 129, 130, 131, 132, 133, 134} 55: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 55: 129, 130, 131, 132, 133} 55: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 55: 129, 130, 131, 132, 133} 55: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 55: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 55: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 55: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 55: 129, 130, 131, 132, 133} 55: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 55: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 55: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 55: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 55: 134, 135, 136, 137, 138, 139, 140, 144} 55: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 55: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 55: 139, 140, 141, 142, 143, 144, 145, 146} 55: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 55: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 55: 142, 143, 144, 145, 146, 147, 148} 55: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 55: 144, 145, 146} 55: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 55: 144, 145, 146} 55: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 55: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 55: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 55: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 55: 144, 145, 146, 147, 148, 149, 150, 154} 55: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 55: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 55: 149, 150, 151, 152, 153, 154, 155} 55: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 55: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 55: 152, 153, 154, 155} 55: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 55: 154, 155} 55: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 55: 154, 155} 55: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 55: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 55: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 55: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 55: 154, 155} 55: excls[155][num=6]={146, 148, 149, 150, 154, 155} 55: Bond: 55: nr: 468 55: iatoms: 55: 0 type=100 (BONDS) 0 1 55: 1 type=100 (BONDS) 0 2 55: 2 type=100 (BONDS) 0 3 55: 3 type=101 (BONDS) 0 4 55: 4 type=102 (BONDS) 4 5 55: 5 type=103 (BONDS) 4 6 55: 6 type=104 (BONDS) 4 22 55: 7 type=102 (BONDS) 6 7 55: 8 type=102 (BONDS) 6 8 55: 9 type=103 (BONDS) 6 9 55: 10 type=102 (BONDS) 9 10 55: 11 type=102 (BONDS) 9 11 55: 12 type=103 (BONDS) 9 12 55: 13 type=102 (BONDS) 12 13 55: 14 type=102 (BONDS) 12 14 55: 15 type=103 (BONDS) 12 15 55: 16 type=102 (BONDS) 15 16 55: 17 type=102 (BONDS) 15 17 55: 18 type=101 (BONDS) 15 18 55: 19 type=100 (BONDS) 18 19 55: 20 type=100 (BONDS) 18 20 55: 21 type=100 (BONDS) 18 21 55: 22 type=105 (BONDS) 22 23 55: 23 type=106 (BONDS) 22 24 55: 24 type=100 (BONDS) 24 25 55: 25 type=107 (BONDS) 24 26 55: 26 type=102 (BONDS) 26 27 55: 27 type=103 (BONDS) 26 28 55: 28 type=104 (BONDS) 26 38 55: 29 type=102 (BONDS) 28 29 55: 30 type=103 (BONDS) 28 30 55: 31 type=103 (BONDS) 28 34 55: 32 type=102 (BONDS) 30 31 55: 33 type=102 (BONDS) 30 32 55: 34 type=102 (BONDS) 30 33 55: 35 type=102 (BONDS) 34 35 55: 36 type=102 (BONDS) 34 36 55: 37 type=102 (BONDS) 34 37 55: 38 type=105 (BONDS) 38 39 55: 39 type=106 (BONDS) 38 40 55: 40 type=100 (BONDS) 40 41 55: 41 type=107 (BONDS) 40 42 55: 42 type=102 (BONDS) 42 43 55: 43 type=103 (BONDS) 42 44 55: 44 type=104 (BONDS) 42 58 55: 45 type=102 (BONDS) 44 45 55: 46 type=102 (BONDS) 44 46 55: 47 type=108 (BONDS) 44 47 55: 48 type=109 (BONDS) 47 48 55: 49 type=109 (BONDS) 47 50 55: 50 type=110 (BONDS) 48 49 55: 51 type=109 (BONDS) 48 52 55: 52 type=110 (BONDS) 50 51 55: 53 type=109 (BONDS) 50 54 55: 54 type=110 (BONDS) 52 53 55: 55 type=109 (BONDS) 52 56 55: 56 type=110 (BONDS) 54 55 55: 57 type=109 (BONDS) 54 56 55: 58 type=110 (BONDS) 56 57 55: 59 type=105 (BONDS) 58 59 55: 60 type=106 (BONDS) 58 60 55: 61 type=100 (BONDS) 60 61 55: 62 type=107 (BONDS) 60 62 55: 63 type=102 (BONDS) 62 63 55: 64 type=102 (BONDS) 62 64 55: 65 type=104 (BONDS) 62 65 55: 66 type=105 (BONDS) 65 66 55: 67 type=106 (BONDS) 65 67 55: 68 type=100 (BONDS) 67 68 55: 69 type=107 (BONDS) 67 69 55: 70 type=102 (BONDS) 69 70 55: 71 type=103 (BONDS) 69 71 55: 72 type=104 (BONDS) 69 89 55: 73 type=102 (BONDS) 71 72 55: 74 type=102 (BONDS) 71 73 55: 75 type=103 (BONDS) 71 74 55: 76 type=102 (BONDS) 74 75 55: 77 type=102 (BONDS) 74 76 55: 78 type=103 (BONDS) 74 77 55: 79 type=102 (BONDS) 77 78 55: 80 type=102 (BONDS) 77 79 55: 81 type=111 (BONDS) 77 80 55: 82 type=100 (BONDS) 80 81 55: 83 type=112 (BONDS) 80 82 55: 84 type=112 (BONDS) 82 83 55: 85 type=112 (BONDS) 82 86 55: 86 type=100 (BONDS) 83 84 55: 87 type=100 (BONDS) 83 85 55: 88 type=100 (BONDS) 86 87 55: 89 type=100 (BONDS) 86 88 55: 90 type=105 (BONDS) 89 90 55: 91 type=106 (BONDS) 89 91 55: 92 type=100 (BONDS) 91 92 55: 93 type=107 (BONDS) 91 93 55: 94 type=102 (BONDS) 93 94 55: 95 type=103 (BONDS) 93 95 55: 96 type=104 (BONDS) 93 100 55: 97 type=102 (BONDS) 95 96 55: 98 type=102 (BONDS) 95 97 55: 99 type=113 (BONDS) 95 98 55: 100 type=114 (BONDS) 98 99 55: 101 type=105 (BONDS) 100 101 55: 102 type=106 (BONDS) 100 102 55: 103 type=100 (BONDS) 102 103 55: 104 type=107 (BONDS) 102 104 55: 105 type=102 (BONDS) 104 105 55: 106 type=103 (BONDS) 104 106 55: 107 type=104 (BONDS) 104 115 55: 108 type=102 (BONDS) 106 107 55: 109 type=102 (BONDS) 106 108 55: 110 type=103 (BONDS) 106 109 55: 111 type=102 (BONDS) 109 110 55: 112 type=102 (BONDS) 109 111 55: 113 type=104 (BONDS) 109 112 55: 114 type=115 (BONDS) 112 113 55: 115 type=115 (BONDS) 112 114 55: 116 type=105 (BONDS) 115 116 55: 117 type=106 (BONDS) 115 117 55: 118 type=100 (BONDS) 117 118 55: 119 type=107 (BONDS) 117 119 55: 120 type=102 (BONDS) 119 120 55: 121 type=103 (BONDS) 119 121 55: 122 type=104 (BONDS) 119 134 55: 123 type=102 (BONDS) 121 122 55: 124 type=102 (BONDS) 121 123 55: 125 type=103 (BONDS) 121 124 55: 126 type=102 (BONDS) 124 125 55: 127 type=103 (BONDS) 124 126 55: 128 type=103 (BONDS) 124 130 55: 129 type=102 (BONDS) 126 127 55: 130 type=102 (BONDS) 126 128 55: 131 type=102 (BONDS) 126 129 55: 132 type=102 (BONDS) 130 131 55: 133 type=102 (BONDS) 130 132 55: 134 type=102 (BONDS) 130 133 55: 135 type=105 (BONDS) 134 135 55: 136 type=106 (BONDS) 134 136 55: 137 type=100 (BONDS) 136 137 55: 138 type=107 (BONDS) 136 138 55: 139 type=102 (BONDS) 138 139 55: 140 type=103 (BONDS) 138 140 55: 141 type=104 (BONDS) 138 144 55: 142 type=102 (BONDS) 140 141 55: 143 type=102 (BONDS) 140 142 55: 144 type=102 (BONDS) 140 143 55: 145 type=105 (BONDS) 144 145 55: 146 type=106 (BONDS) 144 146 55: 147 type=100 (BONDS) 146 147 55: 148 type=107 (BONDS) 146 148 55: 149 type=102 (BONDS) 148 149 55: 150 type=103 (BONDS) 148 150 55: 151 type=104 (BONDS) 148 154 55: 152 type=102 (BONDS) 150 151 55: 153 type=102 (BONDS) 150 152 55: 154 type=102 (BONDS) 150 153 55: 155 type=105 (BONDS) 154 155 55: G96Bond: 55: nr: 0 55: Morse: 55: nr: 0 55: Cubic Bonds: 55: nr: 0 55: Connect Bonds: 55: nr: 0 55: Harmonic Pot.: 55: nr: 0 55: FENE Bonds: 55: nr: 0 55: Tab. Bonds: 55: nr: 0 55: Tab. Bonds NC: 55: nr: 0 55: Restraint Pot.: 55: nr: 0 55: Angle: 55: nr: 1124 55: iatoms: 55: 0 type=116 (ANGLES) 1 0 2 55: 1 type=116 (ANGLES) 1 0 3 55: 2 type=116 (ANGLES) 1 0 4 55: 3 type=116 (ANGLES) 2 0 3 55: 4 type=116 (ANGLES) 2 0 4 55: 5 type=116 (ANGLES) 3 0 4 55: 6 type=116 (ANGLES) 0 4 5 55: 7 type=117 (ANGLES) 0 4 6 55: 8 type=117 (ANGLES) 0 4 22 55: 9 type=118 (ANGLES) 5 4 6 55: 10 type=116 (ANGLES) 5 4 22 55: 11 type=119 (ANGLES) 6 4 22 55: 12 type=118 (ANGLES) 4 6 7 55: 13 type=118 (ANGLES) 4 6 8 55: 14 type=120 (ANGLES) 4 6 9 55: 15 type=121 (ANGLES) 7 6 8 55: 16 type=118 (ANGLES) 7 6 9 55: 17 type=118 (ANGLES) 8 6 9 55: 18 type=118 (ANGLES) 6 9 10 55: 19 type=118 (ANGLES) 6 9 11 55: 20 type=120 (ANGLES) 6 9 12 55: 21 type=121 (ANGLES) 10 9 11 55: 22 type=118 (ANGLES) 10 9 12 55: 23 type=118 (ANGLES) 11 9 12 55: 24 type=118 (ANGLES) 9 12 13 55: 25 type=118 (ANGLES) 9 12 14 55: 26 type=120 (ANGLES) 9 12 15 55: 27 type=121 (ANGLES) 13 12 14 55: 28 type=118 (ANGLES) 13 12 15 55: 29 type=118 (ANGLES) 14 12 15 55: 30 type=118 (ANGLES) 12 15 16 55: 31 type=118 (ANGLES) 12 15 17 55: 32 type=117 (ANGLES) 12 15 18 55: 33 type=121 (ANGLES) 16 15 17 55: 34 type=116 (ANGLES) 16 15 18 55: 35 type=116 (ANGLES) 17 15 18 55: 36 type=116 (ANGLES) 15 18 19 55: 37 type=116 (ANGLES) 15 18 20 55: 38 type=116 (ANGLES) 15 18 21 55: 39 type=116 (ANGLES) 19 18 20 55: 40 type=116 (ANGLES) 19 18 21 55: 41 type=116 (ANGLES) 20 18 21 55: 42 type=122 (ANGLES) 4 22 23 55: 43 type=123 (ANGLES) 4 22 24 55: 44 type=124 (ANGLES) 23 22 24 55: 45 type=125 (ANGLES) 22 24 25 55: 46 type=126 (ANGLES) 22 24 26 55: 47 type=127 (ANGLES) 25 24 26 55: 48 type=116 (ANGLES) 24 26 27 55: 49 type=128 (ANGLES) 24 26 28 55: 50 type=129 (ANGLES) 24 26 38 55: 51 type=118 (ANGLES) 27 26 28 55: 52 type=116 (ANGLES) 27 26 38 55: 53 type=119 (ANGLES) 28 26 38 55: 54 type=118 (ANGLES) 26 28 29 55: 55 type=120 (ANGLES) 26 28 30 55: 56 type=120 (ANGLES) 26 28 34 55: 57 type=118 (ANGLES) 29 28 30 55: 58 type=118 (ANGLES) 29 28 34 55: 59 type=120 (ANGLES) 30 28 34 55: 60 type=118 (ANGLES) 28 30 31 55: 61 type=118 (ANGLES) 28 30 32 55: 62 type=118 (ANGLES) 28 30 33 55: 63 type=121 (ANGLES) 31 30 32 55: 64 type=121 (ANGLES) 31 30 33 55: 65 type=121 (ANGLES) 32 30 33 55: 66 type=118 (ANGLES) 28 34 35 55: 67 type=118 (ANGLES) 28 34 36 55: 68 type=118 (ANGLES) 28 34 37 55: 69 type=121 (ANGLES) 35 34 36 55: 70 type=121 (ANGLES) 35 34 37 55: 71 type=121 (ANGLES) 36 34 37 55: 72 type=122 (ANGLES) 26 38 39 55: 73 type=123 (ANGLES) 26 38 40 55: 74 type=124 (ANGLES) 39 38 40 55: 75 type=125 (ANGLES) 38 40 41 55: 76 type=126 (ANGLES) 38 40 42 55: 77 type=127 (ANGLES) 41 40 42 55: 78 type=116 (ANGLES) 40 42 43 55: 79 type=128 (ANGLES) 40 42 44 55: 80 type=129 (ANGLES) 40 42 58 55: 81 type=118 (ANGLES) 43 42 44 55: 82 type=116 (ANGLES) 43 42 58 55: 83 type=119 (ANGLES) 44 42 58 55: 84 type=118 (ANGLES) 42 44 45 55: 85 type=118 (ANGLES) 42 44 46 55: 86 type=130 (ANGLES) 42 44 47 55: 87 type=121 (ANGLES) 45 44 46 55: 88 type=116 (ANGLES) 45 44 47 55: 89 type=116 (ANGLES) 46 44 47 55: 90 type=131 (ANGLES) 44 47 48 55: 91 type=131 (ANGLES) 44 47 50 55: 92 type=132 (ANGLES) 48 47 50 55: 93 type=133 (ANGLES) 47 48 49 55: 94 type=132 (ANGLES) 47 48 52 55: 95 type=133 (ANGLES) 49 48 52 55: 96 type=133 (ANGLES) 47 50 51 55: 97 type=132 (ANGLES) 47 50 54 55: 98 type=133 (ANGLES) 51 50 54 55: 99 type=133 (ANGLES) 48 52 53 55: 100 type=132 (ANGLES) 48 52 56 55: 101 type=133 (ANGLES) 53 52 56 55: 102 type=133 (ANGLES) 50 54 55 55: 103 type=132 (ANGLES) 50 54 56 55: 104 type=133 (ANGLES) 55 54 56 55: 105 type=132 (ANGLES) 52 56 54 55: 106 type=133 (ANGLES) 52 56 57 55: 107 type=133 (ANGLES) 54 56 57 55: 108 type=122 (ANGLES) 42 58 59 55: 109 type=123 (ANGLES) 42 58 60 55: 110 type=124 (ANGLES) 59 58 60 55: 111 type=125 (ANGLES) 58 60 61 55: 112 type=126 (ANGLES) 58 60 62 55: 113 type=127 (ANGLES) 61 60 62 55: 114 type=116 (ANGLES) 60 62 63 55: 115 type=116 (ANGLES) 60 62 64 55: 116 type=129 (ANGLES) 60 62 65 55: 117 type=121 (ANGLES) 63 62 64 55: 118 type=116 (ANGLES) 63 62 65 55: 119 type=116 (ANGLES) 64 62 65 55: 120 type=122 (ANGLES) 62 65 66 55: 121 type=123 (ANGLES) 62 65 67 55: 122 type=124 (ANGLES) 66 65 67 55: 123 type=125 (ANGLES) 65 67 68 55: 124 type=126 (ANGLES) 65 67 69 55: 125 type=127 (ANGLES) 68 67 69 55: 126 type=116 (ANGLES) 67 69 70 55: 127 type=128 (ANGLES) 67 69 71 55: 128 type=129 (ANGLES) 67 69 89 55: 129 type=118 (ANGLES) 70 69 71 55: 130 type=116 (ANGLES) 70 69 89 55: 131 type=119 (ANGLES) 71 69 89 55: 132 type=118 (ANGLES) 69 71 72 55: 133 type=118 (ANGLES) 69 71 73 55: 134 type=120 (ANGLES) 69 71 74 55: 135 type=121 (ANGLES) 72 71 73 55: 136 type=118 (ANGLES) 72 71 74 55: 137 type=118 (ANGLES) 73 71 74 55: 138 type=118 (ANGLES) 71 74 75 55: 139 type=118 (ANGLES) 71 74 76 55: 140 type=120 (ANGLES) 71 74 77 55: 141 type=121 (ANGLES) 75 74 76 55: 142 type=118 (ANGLES) 75 74 77 55: 143 type=118 (ANGLES) 76 74 77 55: 144 type=118 (ANGLES) 74 77 78 55: 145 type=118 (ANGLES) 74 77 79 55: 146 type=117 (ANGLES) 74 77 80 55: 147 type=121 (ANGLES) 78 77 79 55: 148 type=116 (ANGLES) 78 77 80 55: 149 type=116 (ANGLES) 79 77 80 55: 150 type=134 (ANGLES) 77 80 81 55: 151 type=135 (ANGLES) 77 80 82 55: 152 type=133 (ANGLES) 81 80 82 55: 153 type=131 (ANGLES) 80 82 83 55: 154 type=131 (ANGLES) 80 82 86 55: 155 type=131 (ANGLES) 83 82 86 55: 156 type=133 (ANGLES) 82 83 84 55: 157 type=133 (ANGLES) 82 83 85 55: 158 type=133 (ANGLES) 84 83 85 55: 159 type=133 (ANGLES) 82 86 87 55: 160 type=133 (ANGLES) 82 86 88 55: 161 type=133 (ANGLES) 87 86 88 55: 162 type=122 (ANGLES) 69 89 90 55: 163 type=123 (ANGLES) 69 89 91 55: 164 type=124 (ANGLES) 90 89 91 55: 165 type=125 (ANGLES) 89 91 92 55: 166 type=126 (ANGLES) 89 91 93 55: 167 type=127 (ANGLES) 92 91 93 55: 168 type=116 (ANGLES) 91 93 94 55: 169 type=128 (ANGLES) 91 93 95 55: 170 type=129 (ANGLES) 91 93 100 55: 171 type=118 (ANGLES) 94 93 95 55: 172 type=116 (ANGLES) 94 93 100 55: 173 type=119 (ANGLES) 95 93 100 55: 174 type=118 (ANGLES) 93 95 96 55: 175 type=118 (ANGLES) 93 95 97 55: 176 type=136 (ANGLES) 93 95 98 55: 177 type=121 (ANGLES) 96 95 97 55: 178 type=116 (ANGLES) 96 95 98 55: 179 type=116 (ANGLES) 97 95 98 55: 180 type=137 (ANGLES) 95 98 99 55: 181 type=122 (ANGLES) 93 100 101 55: 182 type=123 (ANGLES) 93 100 102 55: 183 type=124 (ANGLES) 101 100 102 55: 184 type=125 (ANGLES) 100 102 103 55: 185 type=126 (ANGLES) 100 102 104 55: 186 type=127 (ANGLES) 103 102 104 55: 187 type=116 (ANGLES) 102 104 105 55: 188 type=128 (ANGLES) 102 104 106 55: 189 type=129 (ANGLES) 102 104 115 55: 190 type=118 (ANGLES) 105 104 106 55: 191 type=116 (ANGLES) 105 104 115 55: 192 type=119 (ANGLES) 106 104 115 55: 193 type=118 (ANGLES) 104 106 107 55: 194 type=118 (ANGLES) 104 106 108 55: 195 type=120 (ANGLES) 104 106 109 55: 196 type=121 (ANGLES) 107 106 108 55: 197 type=118 (ANGLES) 107 106 109 55: 198 type=118 (ANGLES) 108 106 109 55: 199 type=118 (ANGLES) 106 109 110 55: 200 type=118 (ANGLES) 106 109 111 55: 201 type=119 (ANGLES) 106 109 112 55: 202 type=121 (ANGLES) 110 109 111 55: 203 type=116 (ANGLES) 110 109 112 55: 204 type=116 (ANGLES) 111 109 112 55: 205 type=138 (ANGLES) 109 112 113 55: 206 type=138 (ANGLES) 109 112 114 55: 207 type=139 (ANGLES) 113 112 114 55: 208 type=122 (ANGLES) 104 115 116 55: 209 type=123 (ANGLES) 104 115 117 55: 210 type=124 (ANGLES) 116 115 117 55: 211 type=125 (ANGLES) 115 117 118 55: 212 type=126 (ANGLES) 115 117 119 55: 213 type=127 (ANGLES) 118 117 119 55: 214 type=116 (ANGLES) 117 119 120 55: 215 type=128 (ANGLES) 117 119 121 55: 216 type=129 (ANGLES) 117 119 134 55: 217 type=118 (ANGLES) 120 119 121 55: 218 type=116 (ANGLES) 120 119 134 55: 219 type=119 (ANGLES) 121 119 134 55: 220 type=118 (ANGLES) 119 121 122 55: 221 type=118 (ANGLES) 119 121 123 55: 222 type=120 (ANGLES) 119 121 124 55: 223 type=121 (ANGLES) 122 121 123 55: 224 type=118 (ANGLES) 122 121 124 55: 225 type=118 (ANGLES) 123 121 124 55: 226 type=118 (ANGLES) 121 124 125 55: 227 type=120 (ANGLES) 121 124 126 55: 228 type=120 (ANGLES) 121 124 130 55: 229 type=118 (ANGLES) 125 124 126 55: 230 type=118 (ANGLES) 125 124 130 55: 231 type=120 (ANGLES) 126 124 130 55: 232 type=118 (ANGLES) 124 126 127 55: 233 type=118 (ANGLES) 124 126 128 55: 234 type=118 (ANGLES) 124 126 129 55: 235 type=121 (ANGLES) 127 126 128 55: 236 type=121 (ANGLES) 127 126 129 55: 237 type=121 (ANGLES) 128 126 129 55: 238 type=118 (ANGLES) 124 130 131 55: 239 type=118 (ANGLES) 124 130 132 55: 240 type=118 (ANGLES) 124 130 133 55: 241 type=121 (ANGLES) 131 130 132 55: 242 type=121 (ANGLES) 131 130 133 55: 243 type=121 (ANGLES) 132 130 133 55: 244 type=122 (ANGLES) 119 134 135 55: 245 type=123 (ANGLES) 119 134 136 55: 246 type=124 (ANGLES) 135 134 136 55: 247 type=125 (ANGLES) 134 136 137 55: 248 type=126 (ANGLES) 134 136 138 55: 249 type=127 (ANGLES) 137 136 138 55: 250 type=116 (ANGLES) 136 138 139 55: 251 type=128 (ANGLES) 136 138 140 55: 252 type=129 (ANGLES) 136 138 144 55: 253 type=118 (ANGLES) 139 138 140 55: 254 type=116 (ANGLES) 139 138 144 55: 255 type=119 (ANGLES) 140 138 144 55: 256 type=118 (ANGLES) 138 140 141 55: 257 type=118 (ANGLES) 138 140 142 55: 258 type=118 (ANGLES) 138 140 143 55: 259 type=121 (ANGLES) 141 140 142 55: 260 type=121 (ANGLES) 141 140 143 55: 261 type=121 (ANGLES) 142 140 143 55: 262 type=122 (ANGLES) 138 144 145 55: 263 type=123 (ANGLES) 138 144 146 55: 264 type=124 (ANGLES) 145 144 146 55: 265 type=125 (ANGLES) 144 146 147 55: 266 type=126 (ANGLES) 144 146 148 55: 267 type=127 (ANGLES) 147 146 148 55: 268 type=116 (ANGLES) 146 148 149 55: 269 type=128 (ANGLES) 146 148 150 55: 270 type=129 (ANGLES) 146 148 154 55: 271 type=118 (ANGLES) 149 148 150 55: 272 type=116 (ANGLES) 149 148 154 55: 273 type=119 (ANGLES) 150 148 154 55: 274 type=118 (ANGLES) 148 150 151 55: 275 type=118 (ANGLES) 148 150 152 55: 276 type=118 (ANGLES) 148 150 153 55: 277 type=121 (ANGLES) 151 150 152 55: 278 type=121 (ANGLES) 151 150 153 55: 279 type=121 (ANGLES) 152 150 153 55: 280 type=122 (ANGLES) 148 154 155 55: G96Angle: 55: nr: 0 55: Restr. Angles: 55: nr: 0 55: Lin. Angle: 55: nr: 0 55: Bond-Cross: 55: nr: 0 55: BA-Cross: 55: nr: 0 55: U-B: 55: nr: 0 55: Quartic Angles: 55: nr: 0 55: Tab. Angles: 55: nr: 0 55: Proper Dih.: 55: nr: 145 55: iatoms: 55: 0 type=140 (PDIHS) 4 24 22 23 55: 1 type=141 (PDIHS) 22 26 24 25 55: 2 type=140 (PDIHS) 26 40 38 39 55: 3 type=141 (PDIHS) 38 42 40 41 55: 4 type=140 (PDIHS) 42 60 58 59 55: 5 type=142 (PDIHS) 44 47 50 48 55: 6 type=142 (PDIHS) 47 52 48 49 55: 7 type=142 (PDIHS) 47 54 50 51 55: 8 type=142 (PDIHS) 48 56 52 53 55: 9 type=142 (PDIHS) 50 56 54 55 55: 10 type=142 (PDIHS) 52 54 56 57 55: 11 type=141 (PDIHS) 58 62 60 61 55: 12 type=140 (PDIHS) 62 67 65 66 55: 13 type=141 (PDIHS) 65 69 67 68 55: 14 type=140 (PDIHS) 69 91 89 90 55: 15 type=141 (PDIHS) 77 82 80 81 55: 16 type=140 (PDIHS) 80 83 82 86 55: 17 type=141 (PDIHS) 82 84 83 85 55: 18 type=141 (PDIHS) 82 87 86 88 55: 19 type=141 (PDIHS) 89 93 91 92 55: 20 type=140 (PDIHS) 93 102 100 101 55: 21 type=141 (PDIHS) 100 104 102 103 55: 22 type=140 (PDIHS) 104 117 115 116 55: 23 type=140 (PDIHS) 109 113 112 114 55: 24 type=141 (PDIHS) 115 119 117 118 55: 25 type=140 (PDIHS) 119 136 134 135 55: 26 type=141 (PDIHS) 134 138 136 137 55: 27 type=140 (PDIHS) 138 146 144 145 55: 28 type=141 (PDIHS) 144 148 146 147 55: Ryckaert-Bell.: 55: nr: 1565 55: iatoms: 55: 0 type=143 (RBDIHS) 1 0 4 5 55: 1 type=144 (RBDIHS) 1 0 4 6 55: 2 type=144 (RBDIHS) 1 0 4 22 55: 3 type=143 (RBDIHS) 2 0 4 5 55: 4 type=144 (RBDIHS) 2 0 4 6 55: 5 type=144 (RBDIHS) 2 0 4 22 55: 6 type=143 (RBDIHS) 3 0 4 5 55: 7 type=144 (RBDIHS) 3 0 4 6 55: 8 type=144 (RBDIHS) 3 0 4 22 55: 9 type=145 (RBDIHS) 0 4 6 9 55: 10 type=146 (RBDIHS) 22 4 6 9 55: 11 type=147 (RBDIHS) 0 4 6 7 55: 12 type=147 (RBDIHS) 0 4 6 8 55: 13 type=148 (RBDIHS) 5 4 6 7 55: 14 type=148 (RBDIHS) 5 4 6 8 55: 15 type=148 (RBDIHS) 5 4 6 9 55: 16 type=149 (RBDIHS) 22 4 6 7 55: 17 type=149 (RBDIHS) 22 4 6 8 55: 18 type=150 (RBDIHS) 0 4 22 24 55: 19 type=151 (RBDIHS) 6 4 22 24 55: 20 type=148 (RBDIHS) 4 6 9 10 55: 21 type=148 (RBDIHS) 4 6 9 11 55: 22 type=152 (RBDIHS) 4 6 9 12 55: 23 type=148 (RBDIHS) 7 6 9 10 55: 24 type=148 (RBDIHS) 7 6 9 11 55: 25 type=148 (RBDIHS) 7 6 9 12 55: 26 type=148 (RBDIHS) 8 6 9 10 55: 27 type=148 (RBDIHS) 8 6 9 11 55: 28 type=148 (RBDIHS) 8 6 9 12 55: 29 type=148 (RBDIHS) 6 9 12 13 55: 30 type=148 (RBDIHS) 6 9 12 14 55: 31 type=152 (RBDIHS) 6 9 12 15 55: 32 type=148 (RBDIHS) 10 9 12 13 55: 33 type=148 (RBDIHS) 10 9 12 14 55: 34 type=148 (RBDIHS) 10 9 12 15 55: 35 type=148 (RBDIHS) 11 9 12 13 55: 36 type=148 (RBDIHS) 11 9 12 14 55: 37 type=148 (RBDIHS) 11 9 12 15 55: 38 type=148 (RBDIHS) 9 12 15 16 55: 39 type=148 (RBDIHS) 9 12 15 17 55: 40 type=153 (RBDIHS) 9 12 15 18 55: 41 type=148 (RBDIHS) 13 12 15 16 55: 42 type=148 (RBDIHS) 13 12 15 17 55: 43 type=154 (RBDIHS) 13 12 15 18 55: 44 type=148 (RBDIHS) 14 12 15 16 55: 45 type=148 (RBDIHS) 14 12 15 17 55: 46 type=154 (RBDIHS) 14 12 15 18 55: 47 type=144 (RBDIHS) 12 15 18 19 55: 48 type=144 (RBDIHS) 12 15 18 20 55: 49 type=144 (RBDIHS) 12 15 18 21 55: 50 type=143 (RBDIHS) 16 15 18 19 55: 51 type=143 (RBDIHS) 16 15 18 20 55: 52 type=143 (RBDIHS) 16 15 18 21 55: 53 type=143 (RBDIHS) 17 15 18 19 55: 54 type=143 (RBDIHS) 17 15 18 20 55: 55 type=143 (RBDIHS) 17 15 18 21 55: 56 type=155 (RBDIHS) 4 22 24 25 55: 57 type=156 (RBDIHS) 4 22 24 26 55: 58 type=155 (RBDIHS) 23 22 24 25 55: 59 type=157 (RBDIHS) 23 22 24 26 55: 60 type=158 (RBDIHS) 22 24 26 28 55: 61 type=159 (RBDIHS) 22 24 26 38 55: 62 type=160 (RBDIHS) 24 26 28 30 55: 63 type=160 (RBDIHS) 24 26 28 34 55: 64 type=161 (RBDIHS) 38 26 28 30 55: 65 type=161 (RBDIHS) 38 26 28 34 55: 66 type=147 (RBDIHS) 24 26 28 29 55: 67 type=148 (RBDIHS) 27 26 28 29 55: 68 type=148 (RBDIHS) 27 26 28 30 55: 69 type=148 (RBDIHS) 27 26 28 34 55: 70 type=149 (RBDIHS) 38 26 28 29 55: 71 type=150 (RBDIHS) 24 26 38 40 55: 72 type=151 (RBDIHS) 28 26 38 40 55: 73 type=148 (RBDIHS) 26 28 30 31 55: 74 type=148 (RBDIHS) 26 28 30 32 55: 75 type=148 (RBDIHS) 26 28 30 33 55: 76 type=148 (RBDIHS) 29 28 30 31 55: 77 type=148 (RBDIHS) 29 28 30 32 55: 78 type=148 (RBDIHS) 29 28 30 33 55: 79 type=148 (RBDIHS) 34 28 30 31 55: 80 type=148 (RBDIHS) 34 28 30 32 55: 81 type=148 (RBDIHS) 34 28 30 33 55: 82 type=148 (RBDIHS) 26 28 34 35 55: 83 type=148 (RBDIHS) 26 28 34 36 55: 84 type=148 (RBDIHS) 26 28 34 37 55: 85 type=148 (RBDIHS) 29 28 34 35 55: 86 type=148 (RBDIHS) 29 28 34 36 55: 87 type=148 (RBDIHS) 29 28 34 37 55: 88 type=148 (RBDIHS) 30 28 34 35 55: 89 type=148 (RBDIHS) 30 28 34 36 55: 90 type=148 (RBDIHS) 30 28 34 37 55: 91 type=155 (RBDIHS) 26 38 40 41 55: 92 type=156 (RBDIHS) 26 38 40 42 55: 93 type=155 (RBDIHS) 39 38 40 41 55: 94 type=157 (RBDIHS) 39 38 40 42 55: 95 type=158 (RBDIHS) 38 40 42 44 55: 96 type=159 (RBDIHS) 38 40 42 58 55: 97 type=147 (RBDIHS) 40 42 44 45 55: 98 type=147 (RBDIHS) 40 42 44 46 55: 99 type=162 (RBDIHS) 40 42 44 47 55: 100 type=148 (RBDIHS) 43 42 44 45 55: 101 type=148 (RBDIHS) 43 42 44 46 55: 102 type=163 (RBDIHS) 43 42 44 47 55: 103 type=149 (RBDIHS) 58 42 44 45 55: 104 type=149 (RBDIHS) 58 42 44 46 55: 105 type=164 (RBDIHS) 58 42 44 47 55: 106 type=150 (RBDIHS) 40 42 58 60 55: 107 type=151 (RBDIHS) 44 42 58 60 55: 108 type=165 (RBDIHS) 44 47 48 49 55: 109 type=165 (RBDIHS) 44 47 48 52 55: 110 type=165 (RBDIHS) 50 47 48 49 55: 111 type=165 (RBDIHS) 50 47 48 52 55: 112 type=165 (RBDIHS) 44 47 50 51 55: 113 type=165 (RBDIHS) 44 47 50 54 55: 114 type=165 (RBDIHS) 48 47 50 51 55: 115 type=165 (RBDIHS) 48 47 50 54 55: 116 type=165 (RBDIHS) 47 48 52 53 55: 117 type=165 (RBDIHS) 47 48 52 56 55: 118 type=165 (RBDIHS) 49 48 52 53 55: 119 type=165 (RBDIHS) 49 48 52 56 55: 120 type=165 (RBDIHS) 47 50 54 55 55: 121 type=165 (RBDIHS) 47 50 54 56 55: 122 type=165 (RBDIHS) 51 50 54 55 55: 123 type=165 (RBDIHS) 51 50 54 56 55: 124 type=165 (RBDIHS) 48 52 56 54 55: 125 type=165 (RBDIHS) 48 52 56 57 55: 126 type=165 (RBDIHS) 53 52 56 54 55: 127 type=165 (RBDIHS) 53 52 56 57 55: 128 type=165 (RBDIHS) 50 54 56 52 55: 129 type=165 (RBDIHS) 50 54 56 57 55: 130 type=165 (RBDIHS) 55 54 56 52 55: 131 type=165 (RBDIHS) 55 54 56 57 55: 132 type=155 (RBDIHS) 42 58 60 61 55: 133 type=156 (RBDIHS) 42 58 60 62 55: 134 type=155 (RBDIHS) 59 58 60 61 55: 135 type=157 (RBDIHS) 59 58 60 62 55: 136 type=159 (RBDIHS) 58 60 62 65 55: 137 type=150 (RBDIHS) 60 62 65 67 55: 138 type=155 (RBDIHS) 62 65 67 68 55: 139 type=156 (RBDIHS) 62 65 67 69 55: 140 type=155 (RBDIHS) 66 65 67 68 55: 141 type=157 (RBDIHS) 66 65 67 69 55: 142 type=158 (RBDIHS) 65 67 69 71 55: 143 type=159 (RBDIHS) 65 67 69 89 55: 144 type=166 (RBDIHS) 67 69 71 74 55: 145 type=167 (RBDIHS) 89 69 71 74 55: 146 type=147 (RBDIHS) 67 69 71 72 55: 147 type=147 (RBDIHS) 67 69 71 73 55: 148 type=148 (RBDIHS) 70 69 71 72 55: 149 type=148 (RBDIHS) 70 69 71 73 55: 150 type=148 (RBDIHS) 70 69 71 74 55: 151 type=149 (RBDIHS) 89 69 71 72 55: 152 type=149 (RBDIHS) 89 69 71 73 55: 153 type=150 (RBDIHS) 67 69 89 91 55: 154 type=151 (RBDIHS) 71 69 89 91 55: 155 type=148 (RBDIHS) 69 71 74 75 55: 156 type=148 (RBDIHS) 69 71 74 76 55: 157 type=152 (RBDIHS) 69 71 74 77 55: 158 type=148 (RBDIHS) 72 71 74 75 55: 159 type=148 (RBDIHS) 72 71 74 76 55: 160 type=148 (RBDIHS) 72 71 74 77 55: 161 type=148 (RBDIHS) 73 71 74 75 55: 162 type=148 (RBDIHS) 73 71 74 76 55: 163 type=148 (RBDIHS) 73 71 74 77 55: 164 type=148 (RBDIHS) 71 74 77 78 55: 165 type=148 (RBDIHS) 71 74 77 79 55: 166 type=153 (RBDIHS) 71 74 77 80 55: 167 type=148 (RBDIHS) 75 74 77 78 55: 168 type=148 (RBDIHS) 75 74 77 79 55: 169 type=168 (RBDIHS) 75 74 77 80 55: 170 type=148 (RBDIHS) 76 74 77 78 55: 171 type=148 (RBDIHS) 76 74 77 79 55: 172 type=168 (RBDIHS) 76 74 77 80 55: 173 type=169 (RBDIHS) 74 77 80 81 55: 174 type=170 (RBDIHS) 74 77 80 82 55: 175 type=171 (RBDIHS) 78 77 80 82 55: 176 type=171 (RBDIHS) 79 77 80 82 55: 177 type=172 (RBDIHS) 77 80 82 83 55: 178 type=172 (RBDIHS) 77 80 82 86 55: 179 type=173 (RBDIHS) 81 80 82 83 55: 180 type=173 (RBDIHS) 81 80 82 86 55: 181 type=173 (RBDIHS) 80 82 83 84 55: 182 type=173 (RBDIHS) 80 82 83 85 55: 183 type=173 (RBDIHS) 86 82 83 84 55: 184 type=173 (RBDIHS) 86 82 83 85 55: 185 type=173 (RBDIHS) 80 82 86 87 55: 186 type=173 (RBDIHS) 80 82 86 88 55: 187 type=173 (RBDIHS) 83 82 86 87 55: 188 type=173 (RBDIHS) 83 82 86 88 55: 189 type=155 (RBDIHS) 69 89 91 92 55: 190 type=156 (RBDIHS) 69 89 91 93 55: 191 type=155 (RBDIHS) 90 89 91 92 55: 192 type=157 (RBDIHS) 90 89 91 93 55: 193 type=158 (RBDIHS) 89 91 93 95 55: 194 type=159 (RBDIHS) 89 91 93 100 55: 195 type=174 (RBDIHS) 91 93 95 98 55: 196 type=175 (RBDIHS) 100 93 95 98 55: 197 type=147 (RBDIHS) 91 93 95 96 55: 198 type=147 (RBDIHS) 91 93 95 97 55: 199 type=148 (RBDIHS) 94 93 95 96 55: 200 type=148 (RBDIHS) 94 93 95 97 55: 201 type=176 (RBDIHS) 94 93 95 98 55: 202 type=149 (RBDIHS) 100 93 95 96 55: 203 type=149 (RBDIHS) 100 93 95 97 55: 204 type=150 (RBDIHS) 91 93 100 102 55: 205 type=151 (RBDIHS) 95 93 100 102 55: 206 type=177 (RBDIHS) 93 95 98 99 55: 207 type=178 (RBDIHS) 96 95 98 99 55: 208 type=178 (RBDIHS) 97 95 98 99 55: 209 type=155 (RBDIHS) 93 100 102 103 55: 210 type=156 (RBDIHS) 93 100 102 104 55: 211 type=155 (RBDIHS) 101 100 102 103 55: 212 type=157 (RBDIHS) 101 100 102 104 55: 213 type=158 (RBDIHS) 100 102 104 106 55: 214 type=159 (RBDIHS) 100 102 104 115 55: 215 type=179 (RBDIHS) 102 104 106 109 55: 216 type=180 (RBDIHS) 115 104 106 109 55: 217 type=147 (RBDIHS) 102 104 106 107 55: 218 type=147 (RBDIHS) 102 104 106 108 55: 219 type=148 (RBDIHS) 105 104 106 107 55: 220 type=148 (RBDIHS) 105 104 106 108 55: 221 type=148 (RBDIHS) 105 104 106 109 55: 222 type=149 (RBDIHS) 115 104 106 107 55: 223 type=149 (RBDIHS) 115 104 106 108 55: 224 type=150 (RBDIHS) 102 104 115 117 55: 225 type=151 (RBDIHS) 106 104 115 117 55: 226 type=148 (RBDIHS) 104 106 109 110 55: 227 type=148 (RBDIHS) 104 106 109 111 55: 228 type=181 (RBDIHS) 104 106 109 112 55: 229 type=148 (RBDIHS) 107 106 109 110 55: 230 type=148 (RBDIHS) 107 106 109 111 55: 231 type=182 (RBDIHS) 107 106 109 112 55: 232 type=148 (RBDIHS) 108 106 109 110 55: 233 type=148 (RBDIHS) 108 106 109 111 55: 234 type=182 (RBDIHS) 108 106 109 112 55: 235 type=183 (RBDIHS) 106 109 112 113 55: 236 type=183 (RBDIHS) 106 109 112 114 55: 237 type=155 (RBDIHS) 104 115 117 118 55: 238 type=156 (RBDIHS) 104 115 117 119 55: 239 type=155 (RBDIHS) 116 115 117 118 55: 240 type=157 (RBDIHS) 116 115 117 119 55: 241 type=158 (RBDIHS) 115 117 119 121 55: 242 type=159 (RBDIHS) 115 117 119 134 55: 243 type=184 (RBDIHS) 117 119 121 124 55: 244 type=185 (RBDIHS) 134 119 121 124 55: 245 type=147 (RBDIHS) 117 119 121 122 55: 246 type=147 (RBDIHS) 117 119 121 123 55: 247 type=148 (RBDIHS) 120 119 121 122 55: 248 type=148 (RBDIHS) 120 119 121 123 55: 249 type=148 (RBDIHS) 120 119 121 124 55: 250 type=149 (RBDIHS) 134 119 121 122 55: 251 type=149 (RBDIHS) 134 119 121 123 55: 252 type=150 (RBDIHS) 117 119 134 136 55: 253 type=151 (RBDIHS) 121 119 134 136 55: 254 type=148 (RBDIHS) 119 121 124 125 55: 255 type=152 (RBDIHS) 119 121 124 126 55: 256 type=152 (RBDIHS) 119 121 124 130 55: 257 type=148 (RBDIHS) 122 121 124 125 55: 258 type=148 (RBDIHS) 122 121 124 126 55: 259 type=148 (RBDIHS) 122 121 124 130 55: 260 type=148 (RBDIHS) 123 121 124 125 55: 261 type=148 (RBDIHS) 123 121 124 126 55: 262 type=148 (RBDIHS) 123 121 124 130 55: 263 type=148 (RBDIHS) 121 124 126 127 55: 264 type=148 (RBDIHS) 121 124 126 128 55: 265 type=148 (RBDIHS) 121 124 126 129 55: 266 type=148 (RBDIHS) 125 124 126 127 55: 267 type=148 (RBDIHS) 125 124 126 128 55: 268 type=148 (RBDIHS) 125 124 126 129 55: 269 type=148 (RBDIHS) 130 124 126 127 55: 270 type=148 (RBDIHS) 130 124 126 128 55: 271 type=148 (RBDIHS) 130 124 126 129 55: 272 type=148 (RBDIHS) 121 124 130 131 55: 273 type=148 (RBDIHS) 121 124 130 132 55: 274 type=148 (RBDIHS) 121 124 130 133 55: 275 type=148 (RBDIHS) 125 124 130 131 55: 276 type=148 (RBDIHS) 125 124 130 132 55: 277 type=148 (RBDIHS) 125 124 130 133 55: 278 type=148 (RBDIHS) 126 124 130 131 55: 279 type=148 (RBDIHS) 126 124 130 132 55: 280 type=148 (RBDIHS) 126 124 130 133 55: 281 type=155 (RBDIHS) 119 134 136 137 55: 282 type=156 (RBDIHS) 119 134 136 138 55: 283 type=155 (RBDIHS) 135 134 136 137 55: 284 type=157 (RBDIHS) 135 134 136 138 55: 285 type=158 (RBDIHS) 134 136 138 140 55: 286 type=159 (RBDIHS) 134 136 138 144 55: 287 type=147 (RBDIHS) 136 138 140 141 55: 288 type=147 (RBDIHS) 136 138 140 142 55: 289 type=147 (RBDIHS) 136 138 140 143 55: 290 type=148 (RBDIHS) 139 138 140 141 55: 291 type=148 (RBDIHS) 139 138 140 142 55: 292 type=148 (RBDIHS) 139 138 140 143 55: 293 type=149 (RBDIHS) 144 138 140 141 55: 294 type=149 (RBDIHS) 144 138 140 142 55: 295 type=149 (RBDIHS) 144 138 140 143 55: 296 type=150 (RBDIHS) 136 138 144 146 55: 297 type=151 (RBDIHS) 140 138 144 146 55: 298 type=155 (RBDIHS) 138 144 146 147 55: 299 type=156 (RBDIHS) 138 144 146 148 55: 300 type=155 (RBDIHS) 145 144 146 147 55: 301 type=157 (RBDIHS) 145 144 146 148 55: 302 type=158 (RBDIHS) 144 146 148 150 55: 303 type=159 (RBDIHS) 144 146 148 154 55: 304 type=147 (RBDIHS) 146 148 150 151 55: 305 type=147 (RBDIHS) 146 148 150 152 55: 306 type=147 (RBDIHS) 146 148 150 153 55: 307 type=148 (RBDIHS) 149 148 150 151 55: 308 type=148 (RBDIHS) 149 148 150 152 55: 309 type=148 (RBDIHS) 149 148 150 153 55: 310 type=149 (RBDIHS) 154 148 150 151 55: 311 type=149 (RBDIHS) 154 148 150 152 55: 312 type=149 (RBDIHS) 154 148 150 153 55: Restr. Dih.: 55: nr: 0 55: CBT Dih.: 55: nr: 0 55: Fourier Dih.: 55: nr: 0 55: Improper Dih.: 55: nr: 0 55: Per. Imp. Dih.: 55: nr: 0 55: Tab. Dih.: 55: nr: 0 55: CMAP Dih.: 55: nr: 0 55: GB 1-2 Pol. (unused): 55: nr: 0 55: GB 1-3 Pol. (unused): 55: nr: 0 55: GB 1-4 Pol. (unused): 55: nr: 0 55: GB Polarization (unused): 55: nr: 0 55: Nonpolar Sol. (unused): 55: nr: 0 55: LJ-14: 55: nr: 1197 55: iatoms: 55: 0 type=186 (LJ14) 0 7 55: 1 type=186 (LJ14) 0 8 55: 2 type=187 (LJ14) 0 9 55: 3 type=188 (LJ14) 0 23 55: 4 type=189 (LJ14) 0 24 55: 5 type=190 (LJ14) 1 5 55: 6 type=190 (LJ14) 1 6 55: 7 type=190 (LJ14) 1 22 55: 8 type=190 (LJ14) 2 5 55: 9 type=190 (LJ14) 2 6 55: 10 type=190 (LJ14) 2 22 55: 11 type=190 (LJ14) 3 5 55: 12 type=190 (LJ14) 3 6 55: 13 type=190 (LJ14) 3 22 55: 14 type=191 (LJ14) 4 10 55: 15 type=191 (LJ14) 4 11 55: 16 type=192 (LJ14) 4 12 55: 17 type=190 (LJ14) 4 25 55: 18 type=192 (LJ14) 4 26 55: 19 type=193 (LJ14) 5 7 55: 20 type=193 (LJ14) 5 8 55: 21 type=191 (LJ14) 5 9 55: 22 type=194 (LJ14) 5 23 55: 23 type=186 (LJ14) 5 24 55: 24 type=191 (LJ14) 6 13 55: 25 type=191 (LJ14) 6 14 55: 26 type=192 (LJ14) 6 15 55: 27 type=195 (LJ14) 6 23 55: 28 type=187 (LJ14) 6 24 55: 29 type=193 (LJ14) 7 10 55: 30 type=193 (LJ14) 7 11 55: 31 type=191 (LJ14) 7 12 55: 32 type=196 (LJ14) 7 22 55: 33 type=193 (LJ14) 8 10 55: 34 type=193 (LJ14) 8 11 55: 35 type=191 (LJ14) 8 12 55: 36 type=196 (LJ14) 8 22 55: 37 type=191 (LJ14) 9 16 55: 38 type=191 (LJ14) 9 17 55: 39 type=187 (LJ14) 9 18 55: 40 type=197 (LJ14) 9 22 55: 41 type=193 (LJ14) 10 13 55: 42 type=193 (LJ14) 10 14 55: 43 type=191 (LJ14) 10 15 55: 44 type=193 (LJ14) 11 13 55: 45 type=193 (LJ14) 11 14 55: 46 type=191 (LJ14) 11 15 55: 47 type=190 (LJ14) 12 19 55: 48 type=190 (LJ14) 12 20 55: 49 type=190 (LJ14) 12 21 55: 50 type=193 (LJ14) 13 16 55: 51 type=193 (LJ14) 13 17 55: 52 type=186 (LJ14) 13 18 55: 53 type=193 (LJ14) 14 16 55: 54 type=193 (LJ14) 14 17 55: 55 type=186 (LJ14) 14 18 55: 56 type=190 (LJ14) 16 19 55: 57 type=190 (LJ14) 16 20 55: 58 type=190 (LJ14) 16 21 55: 59 type=190 (LJ14) 17 19 55: 60 type=190 (LJ14) 17 20 55: 61 type=190 (LJ14) 17 21 55: 62 type=196 (LJ14) 22 27 55: 63 type=197 (LJ14) 22 28 55: 64 type=198 (LJ14) 22 38 55: 65 type=190 (LJ14) 23 25 55: 66 type=195 (LJ14) 23 26 55: 67 type=186 (LJ14) 24 29 55: 68 type=187 (LJ14) 24 30 55: 69 type=187 (LJ14) 24 34 55: 70 type=188 (LJ14) 24 39 55: 71 type=189 (LJ14) 24 40 55: 72 type=190 (LJ14) 25 27 55: 73 type=190 (LJ14) 25 28 55: 74 type=190 (LJ14) 25 38 55: 75 type=191 (LJ14) 26 31 55: 76 type=191 (LJ14) 26 32 55: 77 type=191 (LJ14) 26 33 55: 78 type=191 (LJ14) 26 35 55: 79 type=191 (LJ14) 26 36 55: 80 type=191 (LJ14) 26 37 55: 81 type=190 (LJ14) 26 41 55: 82 type=192 (LJ14) 26 42 55: 83 type=193 (LJ14) 27 29 55: 84 type=191 (LJ14) 27 30 55: 85 type=191 (LJ14) 27 34 55: 86 type=194 (LJ14) 27 39 55: 87 type=186 (LJ14) 27 40 55: 88 type=195 (LJ14) 28 39 55: 89 type=187 (LJ14) 28 40 55: 90 type=193 (LJ14) 29 31 55: 91 type=193 (LJ14) 29 32 55: 92 type=193 (LJ14) 29 33 55: 93 type=193 (LJ14) 29 35 55: 94 type=193 (LJ14) 29 36 55: 95 type=193 (LJ14) 29 37 55: 96 type=196 (LJ14) 29 38 55: 97 type=191 (LJ14) 30 35 55: 98 type=191 (LJ14) 30 36 55: 99 type=191 (LJ14) 30 37 55: 100 type=197 (LJ14) 30 38 55: 101 type=191 (LJ14) 31 34 55: 102 type=191 (LJ14) 32 34 55: 103 type=191 (LJ14) 33 34 55: 104 type=197 (LJ14) 34 38 55: 105 type=196 (LJ14) 38 43 55: 106 type=197 (LJ14) 38 44 55: 107 type=198 (LJ14) 38 58 55: 108 type=190 (LJ14) 39 41 55: 109 type=195 (LJ14) 39 42 55: 110 type=186 (LJ14) 40 45 55: 111 type=186 (LJ14) 40 46 55: 112 type=199 (LJ14) 40 47 55: 113 type=188 (LJ14) 40 59 55: 114 type=189 (LJ14) 40 60 55: 115 type=190 (LJ14) 41 43 55: 116 type=190 (LJ14) 41 44 55: 117 type=190 (LJ14) 41 58 55: 118 type=200 (LJ14) 42 48 55: 119 type=200 (LJ14) 42 50 55: 120 type=190 (LJ14) 42 61 55: 121 type=192 (LJ14) 42 62 55: 122 type=193 (LJ14) 43 45 55: 123 type=193 (LJ14) 43 46 55: 124 type=201 (LJ14) 43 47 55: 125 type=194 (LJ14) 43 59 55: 126 type=186 (LJ14) 43 60 55: 127 type=202 (LJ14) 44 49 55: 128 type=202 (LJ14) 44 51 55: 129 type=200 (LJ14) 44 52 55: 130 type=200 (LJ14) 44 54 55: 131 type=195 (LJ14) 44 59 55: 132 type=187 (LJ14) 44 60 55: 133 type=201 (LJ14) 45 48 55: 134 type=201 (LJ14) 45 50 55: 135 type=196 (LJ14) 45 58 55: 136 type=201 (LJ14) 46 48 55: 137 type=201 (LJ14) 46 50 55: 138 type=196 (LJ14) 46 58 55: 139 type=203 (LJ14) 47 53 55: 140 type=203 (LJ14) 47 55 55: 141 type=204 (LJ14) 47 56 55: 142 type=205 (LJ14) 47 58 55: 143 type=203 (LJ14) 48 51 55: 144 type=204 (LJ14) 48 54 55: 145 type=203 (LJ14) 48 57 55: 146 type=203 (LJ14) 49 50 55: 147 type=206 (LJ14) 49 53 55: 148 type=203 (LJ14) 49 56 55: 149 type=204 (LJ14) 50 52 55: 150 type=203 (LJ14) 50 57 55: 151 type=206 (LJ14) 51 55 55: 152 type=203 (LJ14) 51 56 55: 153 type=203 (LJ14) 52 55 55: 154 type=203 (LJ14) 53 54 55: 155 type=206 (LJ14) 53 57 55: 156 type=206 (LJ14) 55 57 55: 157 type=196 (LJ14) 58 63 55: 158 type=196 (LJ14) 58 64 55: 159 type=198 (LJ14) 58 65 55: 160 type=190 (LJ14) 59 61 55: 161 type=195 (LJ14) 59 62 55: 162 type=188 (LJ14) 60 66 55: 163 type=189 (LJ14) 60 67 55: 164 type=190 (LJ14) 61 63 55: 165 type=190 (LJ14) 61 64 55: 166 type=190 (LJ14) 61 65 55: 167 type=190 (LJ14) 62 68 55: 168 type=192 (LJ14) 62 69 55: 169 type=194 (LJ14) 63 66 55: 170 type=186 (LJ14) 63 67 55: 171 type=194 (LJ14) 64 66 55: 172 type=186 (LJ14) 64 67 55: 173 type=196 (LJ14) 65 70 55: 174 type=197 (LJ14) 65 71 55: 175 type=198 (LJ14) 65 89 55: 176 type=190 (LJ14) 66 68 55: 177 type=195 (LJ14) 66 69 55: 178 type=186 (LJ14) 67 72 55: 179 type=186 (LJ14) 67 73 55: 180 type=187 (LJ14) 67 74 55: 181 type=188 (LJ14) 67 90 55: 182 type=189 (LJ14) 67 91 55: 183 type=190 (LJ14) 68 70 55: 184 type=190 (LJ14) 68 71 55: 185 type=190 (LJ14) 68 89 55: 186 type=191 (LJ14) 69 75 55: 187 type=191 (LJ14) 69 76 55: 188 type=192 (LJ14) 69 77 55: 189 type=190 (LJ14) 69 92 55: 190 type=192 (LJ14) 69 93 55: 191 type=193 (LJ14) 70 72 55: 192 type=193 (LJ14) 70 73 55: 193 type=191 (LJ14) 70 74 55: 194 type=194 (LJ14) 70 90 55: 195 type=186 (LJ14) 70 91 55: 196 type=191 (LJ14) 71 78 55: 197 type=191 (LJ14) 71 79 55: 198 type=187 (LJ14) 71 80 55: 199 type=195 (LJ14) 71 90 55: 200 type=187 (LJ14) 71 91 55: 201 type=193 (LJ14) 72 75 55: 202 type=193 (LJ14) 72 76 55: 203 type=191 (LJ14) 72 77 55: 204 type=196 (LJ14) 72 89 55: 205 type=193 (LJ14) 73 75 55: 206 type=193 (LJ14) 73 76 55: 207 type=191 (LJ14) 73 77 55: 208 type=196 (LJ14) 73 89 55: 209 type=190 (LJ14) 74 81 55: 210 type=207 (LJ14) 74 82 55: 211 type=197 (LJ14) 74 89 55: 212 type=193 (LJ14) 75 78 55: 213 type=193 (LJ14) 75 79 55: 214 type=186 (LJ14) 75 80 55: 215 type=193 (LJ14) 76 78 55: 216 type=193 (LJ14) 76 79 55: 217 type=186 (LJ14) 76 80 55: 218 type=187 (LJ14) 77 83 55: 219 type=187 (LJ14) 77 86 55: 220 type=190 (LJ14) 78 81 55: 221 type=208 (LJ14) 78 82 55: 222 type=190 (LJ14) 79 81 55: 223 type=208 (LJ14) 79 82 55: 224 type=190 (LJ14) 80 84 55: 225 type=190 (LJ14) 80 85 55: 226 type=190 (LJ14) 80 87 55: 227 type=190 (LJ14) 80 88 55: 228 type=190 (LJ14) 81 83 55: 229 type=190 (LJ14) 81 86 55: 230 type=190 (LJ14) 83 87 55: 231 type=190 (LJ14) 83 88 55: 232 type=190 (LJ14) 84 86 55: 233 type=190 (LJ14) 85 86 55: 234 type=196 (LJ14) 89 94 55: 235 type=197 (LJ14) 89 95 55: 236 type=198 (LJ14) 89 100 55: 237 type=190 (LJ14) 90 92 55: 238 type=195 (LJ14) 90 93 55: 239 type=186 (LJ14) 91 96 55: 240 type=186 (LJ14) 91 97 55: 241 type=209 (LJ14) 91 98 55: 242 type=188 (LJ14) 91 101 55: 243 type=189 (LJ14) 91 102 55: 244 type=190 (LJ14) 92 94 55: 245 type=190 (LJ14) 92 95 55: 246 type=190 (LJ14) 92 100 55: 247 type=190 (LJ14) 93 99 55: 248 type=190 (LJ14) 93 103 55: 249 type=192 (LJ14) 93 104 55: 250 type=193 (LJ14) 94 96 55: 251 type=193 (LJ14) 94 97 55: 252 type=210 (LJ14) 94 98 55: 253 type=194 (LJ14) 94 101 55: 254 type=186 (LJ14) 94 102 55: 255 type=195 (LJ14) 95 101 55: 256 type=187 (LJ14) 95 102 55: 257 type=190 (LJ14) 96 99 55: 258 type=196 (LJ14) 96 100 55: 259 type=190 (LJ14) 97 99 55: 260 type=196 (LJ14) 97 100 55: 261 type=211 (LJ14) 98 100 55: 262 type=196 (LJ14) 100 105 55: 263 type=197 (LJ14) 100 106 55: 264 type=198 (LJ14) 100 115 55: 265 type=190 (LJ14) 101 103 55: 266 type=195 (LJ14) 101 104 55: 267 type=186 (LJ14) 102 107 55: 268 type=186 (LJ14) 102 108 55: 269 type=187 (LJ14) 102 109 55: 270 type=188 (LJ14) 102 116 55: 271 type=189 (LJ14) 102 117 55: 272 type=190 (LJ14) 103 105 55: 273 type=190 (LJ14) 103 106 55: 274 type=190 (LJ14) 103 115 55: 275 type=191 (LJ14) 104 110 55: 276 type=191 (LJ14) 104 111 55: 277 type=197 (LJ14) 104 112 55: 278 type=190 (LJ14) 104 118 55: 279 type=192 (LJ14) 104 119 55: 280 type=193 (LJ14) 105 107 55: 281 type=193 (LJ14) 105 108 55: 282 type=191 (LJ14) 105 109 55: 283 type=194 (LJ14) 105 116 55: 284 type=186 (LJ14) 105 117 55: 285 type=195 (LJ14) 106 113 55: 286 type=195 (LJ14) 106 114 55: 287 type=195 (LJ14) 106 116 55: 288 type=187 (LJ14) 106 117 55: 289 type=193 (LJ14) 107 110 55: 290 type=193 (LJ14) 107 111 55: 291 type=196 (LJ14) 107 112 55: 292 type=196 (LJ14) 107 115 55: 293 type=193 (LJ14) 108 110 55: 294 type=193 (LJ14) 108 111 55: 295 type=196 (LJ14) 108 112 55: 296 type=196 (LJ14) 108 115 55: 297 type=197 (LJ14) 109 115 55: 298 type=194 (LJ14) 110 113 55: 299 type=194 (LJ14) 110 114 55: 300 type=194 (LJ14) 111 113 55: 301 type=194 (LJ14) 111 114 55: 302 type=196 (LJ14) 115 120 55: 303 type=197 (LJ14) 115 121 55: 304 type=198 (LJ14) 115 134 55: 305 type=190 (LJ14) 116 118 55: 306 type=195 (LJ14) 116 119 55: 307 type=186 (LJ14) 117 122 55: 308 type=186 (LJ14) 117 123 55: 309 type=187 (LJ14) 117 124 55: 310 type=188 (LJ14) 117 135 55: 311 type=189 (LJ14) 117 136 55: 312 type=190 (LJ14) 118 120 55: 313 type=190 (LJ14) 118 121 55: 314 type=190 (LJ14) 118 134 55: 315 type=191 (LJ14) 119 125 55: 316 type=192 (LJ14) 119 126 55: 317 type=192 (LJ14) 119 130 55: 318 type=190 (LJ14) 119 137 55: 319 type=192 (LJ14) 119 138 55: 320 type=193 (LJ14) 120 122 55: 321 type=193 (LJ14) 120 123 55: 322 type=191 (LJ14) 120 124 55: 323 type=194 (LJ14) 120 135 55: 324 type=186 (LJ14) 120 136 55: 325 type=191 (LJ14) 121 127 55: 326 type=191 (LJ14) 121 128 55: 327 type=191 (LJ14) 121 129 55: 328 type=191 (LJ14) 121 131 55: 329 type=191 (LJ14) 121 132 55: 330 type=191 (LJ14) 121 133 55: 331 type=195 (LJ14) 121 135 55: 332 type=187 (LJ14) 121 136 55: 333 type=193 (LJ14) 122 125 55: 334 type=191 (LJ14) 122 126 55: 335 type=191 (LJ14) 122 130 55: 336 type=196 (LJ14) 122 134 55: 337 type=193 (LJ14) 123 125 55: 338 type=191 (LJ14) 123 126 55: 339 type=191 (LJ14) 123 130 55: 340 type=196 (LJ14) 123 134 55: 341 type=197 (LJ14) 124 134 55: 342 type=193 (LJ14) 125 127 55: 343 type=193 (LJ14) 125 128 55: 344 type=193 (LJ14) 125 129 55: 345 type=193 (LJ14) 125 131 55: 346 type=193 (LJ14) 125 132 55: 347 type=193 (LJ14) 125 133 55: 348 type=191 (LJ14) 126 131 55: 349 type=191 (LJ14) 126 132 55: 350 type=191 (LJ14) 126 133 55: 351 type=191 (LJ14) 127 130 55: 352 type=191 (LJ14) 128 130 55: 353 type=191 (LJ14) 129 130 55: 354 type=196 (LJ14) 134 139 55: 355 type=197 (LJ14) 134 140 55: 356 type=198 (LJ14) 134 144 55: 357 type=190 (LJ14) 135 137 55: 358 type=195 (LJ14) 135 138 55: 359 type=186 (LJ14) 136 141 55: 360 type=186 (LJ14) 136 142 55: 361 type=186 (LJ14) 136 143 55: 362 type=188 (LJ14) 136 145 55: 363 type=189 (LJ14) 136 146 55: 364 type=190 (LJ14) 137 139 55: 365 type=190 (LJ14) 137 140 55: 366 type=190 (LJ14) 137 144 55: 367 type=190 (LJ14) 138 147 55: 368 type=192 (LJ14) 138 148 55: 369 type=193 (LJ14) 139 141 55: 370 type=193 (LJ14) 139 142 55: 371 type=193 (LJ14) 139 143 55: 372 type=194 (LJ14) 139 145 55: 373 type=186 (LJ14) 139 146 55: 374 type=195 (LJ14) 140 145 55: 375 type=187 (LJ14) 140 146 55: 376 type=196 (LJ14) 141 144 55: 377 type=196 (LJ14) 142 144 55: 378 type=196 (LJ14) 143 144 55: 379 type=196 (LJ14) 144 149 55: 380 type=197 (LJ14) 144 150 55: 381 type=198 (LJ14) 144 154 55: 382 type=190 (LJ14) 145 147 55: 383 type=195 (LJ14) 145 148 55: 384 type=186 (LJ14) 146 151 55: 385 type=186 (LJ14) 146 152 55: 386 type=186 (LJ14) 146 153 55: 387 type=188 (LJ14) 146 155 55: 388 type=190 (LJ14) 147 149 55: 389 type=190 (LJ14) 147 150 55: 390 type=190 (LJ14) 147 154 55: 391 type=193 (LJ14) 149 151 55: 392 type=193 (LJ14) 149 152 55: 393 type=193 (LJ14) 149 153 55: 394 type=194 (LJ14) 149 155 55: 395 type=195 (LJ14) 150 155 55: 396 type=196 (LJ14) 151 154 55: 397 type=196 (LJ14) 152 154 55: 398 type=196 (LJ14) 153 154 55: Coulomb-14: 55: nr: 0 55: LJC-14 q: 55: nr: 0 55: LJC Pairs NB: 55: nr: 0 55: LJ (SR): 55: nr: 0 55: Buck.ham (SR): 55: nr: 0 55: LJ (unused): 55: nr: 0 55: B.ham (unused): 55: nr: 0 55: Disper. corr.: 55: nr: 0 55: Coulomb (SR): 55: nr: 0 55: Coul (unused): 55: nr: 0 55: RF excl.: 55: nr: 0 55: Coul. recip.: 55: nr: 0 55: LJ recip.: 55: nr: 0 55: DPD: 55: nr: 0 55: Polarization: 55: nr: 0 55: Water Pol.: 55: nr: 0 55: Thole Pol.: 55: nr: 0 55: Anharm. Pol.: 55: nr: 0 55: Position Rest.: 55: nr: 0 55: Flat-b. P-R.: 55: nr: 0 55: Dis. Rest.: 55: nr: 0 55: D.R.Viol. (nm): 55: nr: 0 55: Orient. Rest.: 55: nr: 0 55: Ori. R. RMSD: 55: nr: 0 55: Angle Rest.: 55: nr: 0 55: Angle Rest. Z: 55: nr: 0 55: Dih. Rest.: 55: nr: 0 55: Dih. Rest. Viol.: 55: nr: 0 55: Constraint: 55: nr: 0 55: Constr. No Conn.: 55: nr: 0 55: Settle: 55: nr: 0 55: Virtual site 1: 55: nr: 0 55: Virtual site 2: 55: nr: 0 55: Virtual site 2fd: 55: nr: 0 55: Virtual site 3: 55: nr: 0 55: Virtual site 3fd: 55: nr: 0 55: Virtual site 3fad: 55: nr: 0 55: Virtual site 3out: 55: nr: 0 55: Virtual site 4fd: 55: nr: 0 55: Virtual site 4fdn: 55: nr: 0 55: Virtual site N: 55: nr: 0 55: COM Pull En.: 55: nr: 0 55: Dens. fitting: 55: nr: 0 55: Quantum En.: 55: nr: 0 55: Potential: 55: nr: 0 55: Kinetic En.: 55: nr: 0 55: Total Energy: 55: nr: 0 55: Conserved En.: 55: nr: 0 55: Temperature: 55: nr: 0 55: Vir. Temp. (not used): 55: nr: 0 55: Pres. DC: 55: nr: 0 55: Pressure: 55: nr: 0 55: dH/dl constr.: 55: nr: 0 55: dVremain/dl: 55: nr: 0 55: dEkin/dl: 55: nr: 0 55: dVcoul/dl: 55: nr: 0 55: dVvdw/dl: 55: nr: 0 55: dVbonded/dl: 55: nr: 0 55: dVrestraint/dl: 55: nr: 0 55: dVtemperature/dl: 55: nr: 0 55: grp[T-Coupling ] nr=1, name=[ rest] 55: grp[Energy Mon. ] nr=1, name=[ rest] 55: grp[Acc. not used] nr=1, name=[ rest] 55: grp[Freeze ] nr=1, name=[ rest] 55: grp[User1 ] nr=1, name=[ rest] 55: grp[User2 ] nr=1, name=[ rest] 55: grp[VCM ] nr=1, name=[ rest] 55: grp[Compressed X] nr=1, name=[ rest] 55: grp[Or. Res. Fit] nr=1, name=[ rest] 55: grp[QMMM ] nr=1, name=[ rest] 55: grpname (11): 55: grpname[0]={name="System"} 55: grpname[1]={name="Protein"} 55: grpname[2]={name="Protein-H"} 55: grpname[3]={name="C-alpha"} 55: grpname[4]={name="Backbone"} 55: grpname[5]={name="MainChain"} 55: grpname[6]={name="MainChain+Cb"} 55: grpname[7]={name="MainChain+H"} 55: grpname[8]={name="SideChain"} 55: grpname[9]={name="SideChain-H"} 55: grpname[10]={name="rest"} 55: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 55: allocated 0 0 0 0 0 0 0 0 0 0 55: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 55: box (3x3): 55: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 55: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 55: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 55: box_rel (3x3): 55: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: boxv (3x3): 55: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: pres_prev (3x3): 55: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: svir_prev (3x3): 55: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: fvir_prev (3x3): 55: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: nosehoover_xi: not available 55: x (156x3): 55: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 55: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 55: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 55: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 55: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 55: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 55: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 55: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 55: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 55: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 55: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 55: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 55: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 55: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 55: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 55: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 55: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 55: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 55: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 55: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 55: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 55: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 55: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 55: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 55: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 55: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 55: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 55: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 55: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 55: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 55: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 55: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 55: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 55: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 55: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 55: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 55: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 55: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 55: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 55: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 55: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 55: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 55: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 55: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 55: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 55: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 55: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 55: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 55: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 55: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 55: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 55: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 55: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 55: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 55: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 55: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 55: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 55: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 55: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 55: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 55: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 55: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 55: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 55: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 55: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 55: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 55: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 55: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 55: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 55: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 55: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 55: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 55: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 55: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 55: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 55: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 55: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 55: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 55: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 55: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 55: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 55: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 55: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 55: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 55: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 55: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 55: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 55: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 55: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 55: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 55: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 55: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 55: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 55: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 55: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 55: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 55: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 55: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 55: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 55: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 55: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 55: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 55: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 55: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 55: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 55: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 55: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 55: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 55: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 55: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 55: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 55: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 55: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 55: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 55: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 55: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 55: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 55: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 55: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 55: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 55: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 55: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 55: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 55: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 55: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 55: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 55: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 55: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 55: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 55: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 55: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 55: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 55: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 55: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 55: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 55: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 55: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 55: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 55: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 55: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 55: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 55: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 55: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 55: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 55: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 55: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 55: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 55: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 55: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 55: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 55: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 55: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 55: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 55: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 55: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 55: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 55: v (156x3): 55: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: Group statistics 55: T-Coupling : 156 (total 156 atoms) 55: Energy Mon. : 156 (total 156 atoms) 55: Acc. not used: 156 (total 156 atoms) 55: Freeze : 156 (total 156 atoms) 55: User1 : 156 (total 156 atoms) 55: User2 : 156 (total 156 atoms) 55: VCM : 156 (total 156 atoms) 55: Compressed X: 156 (total 156 atoms) 55: Or. Res. Fit: 156 (total 156 atoms) 55: QMMM : 156 (total 156 atoms) 55: [ OK ] DumpTest.WorksWithTpr (21 ms) 55: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: [ OK ] DumpTest.WorksWithTprAndMdpWriting (1 ms) 55: [----------] 2 tests from DumpTest (23 ms total) 55: 55: [----------] 3 tests from HelpwritingTest 55: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 55: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 55: [ RUN ] HelpwritingTest.DumpWritesHelp 55: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 55: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 55: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 55: [----------] 3 tests from HelpwritingTest (1 ms total) 55: 55: [----------] 4 tests from ReportMethodsTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Setting the LD random seed to -14190081 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 55: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 55: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 55: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 55: [ RUN ] ReportMethodsTest.WritesCorrectInformation 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: [ OK ] ReportMethodsTest.WritesCorrectInformation (1 ms) 55: [ RUN ] ReportMethodsTest.ToolEndToEndTest 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: section: Methods 55: subsection: Simulation system 55: A system of 1 molecules (156 atoms) was simulated. 55: 55: subsection: Simulation settings 55: A total of 0 ns were simulated with a time step of 1 fs. 55: Neighbor searching was performed every 10 steps. 55: The Cut-off algorithm was used for electrostatic interactions. 55: with a cut-off of 1 nm. 55: A single cut-off of 1.1 nm was used for Van der Waals interactions. 55: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 55: [----------] 4 tests from ReportMethodsTest (2 ms total) 55: 55: [----------] 3 tests from ConvertTprTest 55: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Setting the LD random seed to -533577 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 0 55: Runtime for the run 0 ps 55: Run end step 0 55: Run end time 0 ps 55: 55: Extending remaining runtime by 100 ps 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 100000 55: Runtime for the run 100 ps 55: Run end step 100000 55: Run end time 100 ps 55: 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 100000 55: Runtime for the run 100 ps 55: Run end step 100000 55: Run end time 100 ps 55: 55: Extending remaining runtime by 100 ps 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 200000 55: Runtime for the run 200 ps 55: Run end step 200000 55: Run end time 200 ps 55: 55: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (570 ms) 55: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Setting the LD random seed to -941761026 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 0 55: Runtime for the run 0 ps 55: Run end step 0 55: Run end time 0 ps 55: 55: Extending remaining runtime to 100 ps 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 100000 55: Runtime for the run 100 ps 55: Run end step 100000 55: Run end time 100 ps 55: 55: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (624 ms) 55: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Setting nsteps to 102 55: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 55: Setting the LD random seed to -537070081 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 0 55: Runtime for the run 0 ps 55: Run end step 0 55: Run end time 0 ps 55: 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 102 55: Runtime for the run 0.102 ps 55: Run end step 102 55: Run end time 0.102 ps 55: 55: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (583 ms) 55: [----------] 3 tests from ConvertTprTest (1778 ms total) 55: 55: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: trr version: GMX_trn_file (single precision) 55: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (1 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (9 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (1 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (5 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 55: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (24 ms total) 55: 55: [----------] 30 tests from Works/TrjconvDumpTest 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (8 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (9 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (5 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (5 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (8 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 55: [----------] 30 tests from Works/TrjconvDumpTest (55 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 54 tests from 6 test suites ran. (3621 ms total) 55: [ PASSED ] 54 tests. 55/81 Test #55: ToolUnitTests .................................. Passed 3.70 sec test 56 Start 56: FileIOTests 56: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/FileIOTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/fileio/tests 56: Test timeout computed to be: 30 56: [==========] Running 42 tests from 10 test suites. 56: [----------] Global test environment set-up. 56: [----------] 4 tests from Checkpoint 56: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 56: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 56: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 56: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 56: [ RUN ] Checkpoint.KvtRoundTripInt64 56: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 56: [ RUN ] Checkpoint.KvtRoundTripReal 56: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 56: [----------] 4 tests from Checkpoint (0 ms total) 56: 56: [----------] 2 tests from FileMD5Test 56: [ RUN ] FileMD5Test.CanComputeMD5 56: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 56: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 56: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 56: [----------] 2 tests from FileMD5Test (1 ms total) 56: 56: [----------] 3 tests from MrcSerializer 56: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 56: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 56: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 56: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 56: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 56: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 56: [----------] 3 tests from MrcSerializer (0 ms total) 56: 56: [----------] 4 tests from MrcDensityMap 56: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 56: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 56: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 56: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 56: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 56: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 56: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 56: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (2 ms) 56: [----------] 4 tests from MrcDensityMap (3 ms total) 56: 56: [----------] 8 tests from MrcDensityMapHeaderTest 56: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 56: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 56: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 56: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.IsSane 56: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 56: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 56: 56: [----------] 10 tests from ReadTest 56: [ RUN ] ReadTest.get_eint_ReadsInteger 56: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 56: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side '0.8' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 56: [ RUN ] ReadTest.get_eint_WarnsAboutString 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side 'hello' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 56: [ RUN ] ReadTest.get_eint64_ReadsInteger 56: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 56: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side '0.8' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 56: [ RUN ] ReadTest.get_eint64_WarnsAboutString 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side 'hello' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 56: [ RUN ] ReadTest.get_ereal_ReadsInteger 56: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 56: [ RUN ] ReadTest.get_ereal_ReadsFloat 56: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 56: [ RUN ] ReadTest.get_ereal_WarnsAboutString 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side 'hello' for parameter 'test' in parameter file is not a 56: real value 56: 56: 56: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 56: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 56: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 56: [----------] 10 tests from ReadTest (0 ms total) 56: 56: [----------] 1 test from FileIOXdrSerializerTest 56: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 56: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 56: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 56: 56: [----------] 2 tests from TngTest 56: [ RUN ] TngTest.CanOpenTngFile 56: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 56: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 56: [ OK ] TngTest.CanOpenTngFile (0 ms) 56: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 56: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 56: [----------] 2 tests from TngTest (0 ms total) 56: 56: [----------] 4 tests from XvgioTest 56: [ RUN ] XvgioTest.readXvgIntWorks 56: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 56: [ RUN ] XvgioTest.readXvgRealWorks 56: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 56: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 56: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 56: [ RUN ] XvgioTest.readXvgDeprecatedWorks 56: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 56: [----------] 4 tests from XvgioTest (0 ms total) 56: 56: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 56: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (2 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 42 tests from 10 test suites ran. (8 ms total) 56: [ PASSED ] 42 tests. 56/81 Test #56: FileIOTests .................................... Passed 0.03 sec test 57 Start 57: SelectionUnitTests 57: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/gromacs/selection/tests 57: Test timeout computed to be: 30 57: [==========] Running 201 tests from 11 test suites. 57: [----------] Global test environment set-up. 57: [----------] 1 test from IndexGroupTest 57: [ RUN ] IndexGroupTest.RemovesDuplicates 57: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 57: [----------] 1 test from IndexGroupTest (0 ms total) 57: 57: [----------] 15 tests from IndexBlockTest 57: [ RUN ] IndexBlockTest.CreatesUnknownBlock 57: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 57: [ RUN ] IndexBlockTest.CreatesAtomBlock 57: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 57: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 57: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 57: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 57: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 57: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 57: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 57: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 57: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 57: [ RUN ] IndexBlockTest.CreatesSingleBlock 57: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 57: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 57: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 57: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 57: [----------] 15 tests from IndexBlockTest (1 ms total) 57: 57: [----------] 11 tests from IndexMapTest 57: [ RUN ] IndexMapTest.InitializesAtomBlock 57: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 57: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 57: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 57: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 57: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 57: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 57: [ RUN ] IndexMapTest.InitializesMoleculeBlock 57: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 57: [ RUN ] IndexMapTest.MapsSingleBlock 57: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 57: [ RUN ] IndexMapTest.MapsResidueBlocks 57: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 57: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 57: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 57: [ RUN ] IndexMapTest.HandlesMultipleRequests 57: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 57: [----------] 11 tests from IndexMapTest (2 ms total) 57: 57: [----------] 3 tests from IndexGroupsAndNamesTest 57: [ RUN ] IndexGroupsAndNamesTest.containsNames 57: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 57: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 57: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 57: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 57: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 57: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 57: 57: [----------] 15 tests from NeighborhoodSearchTest 57: [ RUN ] NeighborhoodSearchTest.SimpleSearch 57: [ OK ] NeighborhoodSearchTest.SimpleSearch (48 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 57: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (51 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchBox 57: [ OK ] NeighborhoodSearchTest.GridSearchBox (10 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 57: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (24 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 57: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (18 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 57: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (1 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 57: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (11 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (137 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 57: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 57: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 57: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 57: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 57: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (12 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 57: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 57: [----------] 15 tests from NeighborhoodSearchTest (319 ms total) 57: 57: [----------] 13 tests from PositionCalculationTest 57: [ RUN ] PositionCalculationTest.ComputesAtomPositions 57: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 57: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 57: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 57: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 57: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 57: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 57: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (4 ms) 57: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 57: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesPositionMask 57: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 57: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 57: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 57: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 57: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 57: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 57: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 57: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 57: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 57: [----------] 13 tests from PositionCalculationTest (8 ms total) 57: 57: [----------] 33 tests from SelectionCollectionTest 57: [ RUN ] SelectionCollectionTest.HandlesNoSelections 57: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 57: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 57: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 57: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (8 ms) 57: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 57: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 57: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 57: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 57: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 57: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 57: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 57: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 57: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 57: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 57: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 57: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 57: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 57: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (8 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 57: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 57: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 57: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 57: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (4 ms) 57: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 57: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 57: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 57: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 57: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 57: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 57: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 57: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 57: [----------] 33 tests from SelectionCollectionTest (35 ms total) 57: 57: [----------] 14 tests from SelectionCollectionInteractiveTest 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 57: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (8 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 57: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 57: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 57: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 57: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 57: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 57: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (4 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 57: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 57: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 57: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 57: [----------] 14 tests from SelectionCollectionInteractiveTest (20 ms total) 57: 57: [----------] 70 tests from SelectionCollectionDataTest 57: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 57: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 57: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesResnr 57: [ OK ] SelectionCollectionDataTest.HandlesResnr (4 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 57: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 57: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 57: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 57: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 57: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (8 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesChain 57: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMass 57: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesCharge 57: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 57: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 57: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 57: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBeta 57: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesResname 57: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 57: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 57: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 57: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (8 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 57: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (13 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (2 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (2 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 57: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (10 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (6 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 57: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 57: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 57: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 57: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 57: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 57: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (9 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 57: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 57: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 57: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 57: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 57: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 57: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 57: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 57: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 57: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 57: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 57: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 57: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (9 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 57: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (5 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (5 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 57: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 57: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 57: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (9 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 57: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 57: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 57: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 57: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (10 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (2 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (10 ms) 57: [----------] 70 tests from SelectionCollectionDataTest (190 ms total) 57: 57: [----------] 17 tests from SelectionOptionTest 57: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 57: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 57: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 57: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 57: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 57: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 57: [ RUN ] SelectionOptionTest.ChecksEmptySelections 57: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 57: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 57: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooManySelections 57: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 57: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 57: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesAdjuster 57: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 57: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 57: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 57: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 57: [----------] 17 tests from SelectionOptionTest (6 ms total) 57: 57: [----------] 9 tests from SelectionFileOptionTest 57: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 57: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (8 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 57: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 57: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 57: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 57: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 57: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 57: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 57: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 57: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 57: [----------] 9 tests from SelectionFileOptionTest (11 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 201 tests from 11 test suites ran. (598 ms total) 57: [ PASSED ] 201 tests. 57/81 Test #57: SelectionUnitTests ............................. Passed 0.68 sec test 58 Start 58: MdrunOutputTests 58: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 58: Test timeout computed to be: 600 58: [==========] Running 12 tests from 5 test suites. 58: [----------] Global test environment set-up. 58: [----------] 1 test from MdrunTest 58: [ RUN ] MdrunTest.WritesHelp 58: [ OK ] MdrunTest.WritesHelp (151 ms) 58: [----------] 1 test from MdrunTest (151 ms total) 58: 58: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 58: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 58: Generating 1-4 interactions: fudge = 0.5 58: Number of degrees of freedom in T-Coupling group rest is 9.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 58: NVE simulation: will use the initial temperature of 2573.591 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 2 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc2' 58: 1 steps, 0.0 ps. 58: Setting the LD random seed to -8912897 58: 58: Generated 3 of the 3 non-bonded parameter combinations 58: 58: Generated 3 of the 3 1-4 parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.006 0.003 195.5 58: (ns/day) (hour/ns) 58: Performance: 52.311 0.459 58: Reading frame 0 time 0.000 58: # Atoms 6 58: Reading frame 1 time 0.001 Last frame 1 time 0.001 58: 58: 58: Item #frames Timestep (ps) 58: Step 2 0.001 58: Time 2 0.001 58: Lambda 0 58: Coords 2 0.001 58: Velocities 0 58: Forces 0 58: Box 2 0.001 58: Checking file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 58: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (124 ms) 58: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 58: Generating 1-4 interactions: fudge = 0.5 58: Number of degrees of freedom in T-Coupling group rest is 9.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 58: NVE simulation: will use the initial temperature of 2573.591 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 2 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc2' 58: 1 steps, 0.0 ps. 58: Setting the LD random seed to 1467383215 58: 58: Generated 3 of the 3 non-bonded parameter combinations 58: 58: Generated 3 of the 3 1-4 parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.003 0.001 190.4 58: (ns/day) (hour/ns) 58: Performance: 129.795 0.185 58: Reading frame 0 time 0.000 58: # Atoms 6 58: Reading frame 1 time 0.001 Last frame 1 time 0.001 58: 58: 58: Item #frames Timestep (ps) 58: Step 2 0.001 58: Time 2 0.001 58: Lambda 0 58: Coords 2 0.001 58: Velocities 0 58: Forces 0 58: Box 2 0.001 58: Checking file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 58: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (38 ms) 58: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 58: Generating 1-4 interactions: fudge = 0.5 58: Number of degrees of freedom in T-Coupling group rest is 9.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 58: NVE simulation: will use the initial temperature of 2573.591 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 2 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc2' 58: 1 steps, 0.0 ps. 58: Setting the LD random seed to 1994292990 58: 58: Generated 3 of the 3 non-bonded parameter combinations 58: 58: Generated 3 of the 3 1-4 parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.003 0.001 188.2 58: (ns/day) (hour/ns) 58: Performance: 124.212 0.193 58: Reading frame 0 time 0.000 58: # Atoms 3 58: Reading frame 1 time 0.001 Last frame 1 time 0.001 58: 58: 58: Item #frames Timestep (ps) 58: Step 2 0.001 58: Time 2 0.001 58: Lambda 0 58: Coords 2 0.001 58: Velocities 0 58: Forces 0 58: Box 2 0.001 58: Checking file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 58: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (31 ms) 58: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (195 ms total) 58: 58: [----------] 2 tests from Argon12/OutputFiles 58: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 58: that with the Verlet scheme, nstlist has no effect on the accuracy of 58: your simulation. 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 58: Setting nstcalcenergy (100) equal to nstenergy (4) 58: 58: Number of degrees of freedom in T-Coupling group System is 33.00 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 58: NVE simulation: will use the initial temperature of 68.810 K for 58: determining the Verlet buffer size 58: 58: 58: There were 3 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'Argon' 58: 16 steps, 0.0 ps. 58: Generated 1 of the 1 non-bonded parameter combinations 58: 58: Excluding 1 bonded neighbours molecule type 'Argon' 58: 58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.004 0.002 192.7 58: (ns/day) (hour/ns) 58: Performance: 690.804 0.035 58: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (31 ms) 58: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 58: that with the Verlet scheme, nstlist has no effect on the accuracy of 58: your simulation. 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 58: Setting nstcalcenergy (100) equal to nstenergy (4) 58: 58: Number of degrees of freedom in T-Coupling group System is 33.00 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 58: NVE simulation: will use the initial temperature of 68.810 K for 58: determining the Verlet buffer size 58: 58: 58: There were 3 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'Argon' 58: 16 steps, 0.0 ps. 58: Generated 1 of the 1 non-bonded parameter combinations 58: 58: Excluding 1 bonded neighbours molecule type 'Argon' 58: 58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.051 0.026 199.6 58: (ns/day) (hour/ns) 58: Performance: 57.136 0.420 58: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (73 ms) 58: [----------] 2 tests from Argon12/OutputFiles (105 ms total) 58: 58: [----------] 3 tests from MdrunCanWrite/Trajectories 58: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 58: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 6 steps, 0.0 ps. 58: Setting the LD random seed to 2113920434 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.055 0.028 199.3 58: (ns/day) (hour/ns) 58: Performance: 21.980 1.092 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (57 ms) 58: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 58: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 6 steps, 0.0 ps. 58: Setting the LD random seed to -270151945 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.063 0.032 199.3 58: (ns/day) (hour/ns) 58: Performance: 19.094 1.257 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (68 ms) 58: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 58: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 6 steps, 0.0 ps. 58: Setting the LD random seed to 1744817901 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.046 0.023 199.1 58: (ns/day) (hour/ns) 58: Performance: 26.148 0.918 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (55 ms) 58: [----------] 3 tests from MdrunCanWrite/Trajectories (181 ms total) 58: 58: [----------] 3 tests from MdrunCanWrite/NptTrajectories 58: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 58: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 2 steps, 0.0 ps. 58: Setting the LD random seed to -604053511 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.046 0.023 199.1 58: (ns/day) (hour/ns) 58: Performance: 11.124 2.157 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (48 ms) 58: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 58: 58: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 58: The Berendsen barostat does not generate any strictly correct ensemble, 58: and should not be used for new production simulations (in our opinion). 58: For isotropic scaling we would recommend the C-rescale barostat that also 58: ensures fast relaxation without oscillations, and for anisotropic scaling 58: you likely want to use the Parrinello-Rahman barostat. 58: 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: 58: There was 1 warning 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 58: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 2 steps, 0.0 ps. 58: Setting the LD random seed to -23076865 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.004 0.002 190.6 58: (ns/day) (hour/ns) 58: Performance: 131.538 0.182 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (18 ms) 58: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 58: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 58: 58: Using 1 MPI thread 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 2 steps, 0.0 ps. 58: Setting the LD random seed to -437266503 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.004 0.002 190.9 58: (ns/day) (hour/ns) 58: Performance: 124.947 0.192 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (18 ms) 58: [----------] 3 tests from MdrunCanWrite/NptTrajectories (86 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 12 tests from 5 test suites ran. (1395 ms total) 58: [ PASSED ] 12 tests. 58/81 Test #58: MdrunOutputTests ............................... Passed 1.45 sec test 59 Start 59: MdrunModulesTests 59: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 59: Test timeout computed to be: 600 59: [==========] Running 15 tests from 3 test suites. 59: [----------] Global test environment set-up. 59: [----------] 9 tests from DensityFittingTest 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -3.85652562592421e+03 59: Maximum force = 4.50998690851897e+03 on atom 3 59: Norm of force = 1.68168494163492e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 1575974621 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (45 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -9.82077921283928e+03 59: Maximum force = 7.39548334240075e+03 on atom 2 59: Norm of force = 2.78250777177324e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1703040010 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (28 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 59: 59: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1124:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (25 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Overriding nsteps with value passed on the command line: 4 steps 59: 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 4 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 5 steps. 59: Potential Energy = -1.09549987768583e+04 59: Maximum force = 7.47247842297766e+03 on atom 2 59: Norm of force = 2.77579925913607e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -1619150363 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (20 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 59: 59: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1124:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (9 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -3.85652562592421e+03 59: Maximum force = 4.50998690851897e+03 on atom 3 59: Norm of force = 1.68168494163492e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -36721161 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (23 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -2.71386626041483e+04 59: Maximum force = 6.78276504921089e+03 on atom 2 59: Norm of force = 1.96088640980697e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -618168857 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (12 ms) 59: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 59: 59: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1124:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/master/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 59: Setting the LD random seed to -1635319809 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (9 ms) 59: [ RUN ] DensityFittingTest.CheckpointWorks 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 59: Setting nstcalcenergy (100) equal to nstenergy (2) 59: 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 59: NVE simulation: will use the initial temperature of 68.810 K for 59: determining the Verlet buffer size 59: 59: 59: There were 2 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting mdrun 'Argon' 59: 2 steps, 0.0 ps. 59: Setting the LD random seed to 1043591143 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 59: 59: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 59: 59: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 59: 59: Note that mdrun will redetermine rlist based on the actual pair-list setup 59: 59: This run will generate roughly 0 Mb of data 59: 59: Writing final coordinates. 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.006 0.003 194.9 59: (ns/day) (hour/ns) 59: Performance: 78.963 0.304 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 59: Can not increase nstlist because an NVE ensemble is used 59: 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting mdrun 'Argon' 59: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 59: 59: Writing final coordinates. 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.024 0.012 198.6 59: (ns/day) (hour/ns) 59: Performance: 35.902 0.668 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (32 ms) 59: [----------] 9 tests from DensityFittingTest (208 ms total) 59: 59: [----------] 4 tests from MimicTest 59: [ RUN ] MimicTest.OneQuantumMol 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 21.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 59: NVE simulation with an initial temperature of zero: will use a Verlet 59: buffer of 10%. Check your energy drift! 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 59: 59: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: NOTE: 19 % of the run time was spent in pair search, 59: you might want to increase nstlist (this has no effect on accuracy) 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.001 0.000 188.4 59: (ns/day) (hour/ns) 59: Performance: 233.347 0.103 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -93335561 59: 59: Generated 10 of the 10 non-bonded parameter combinations 59: 59: Generated 10 of the 10 1-4 parameter combinations 59: 59: Excluding 2 bonded neighbours molecule type 'SOL' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.OneQuantumMol (27 ms) 59: [ RUN ] MimicTest.AllQuantumMol 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 21.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 59: NVE simulation with an initial temperature of zero: will use a Verlet 59: buffer of 10%. Check your energy drift! 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 59: 59: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: NOTE: 19 % of the run time was spent in pair search, 59: you might want to increase nstlist (this has no effect on accuracy) 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.001 0.000 187.9 59: (ns/day) (hour/ns) 59: Performance: 201.551 0.119 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1612812683 59: 59: Generated 10 of the 10 non-bonded parameter combinations 59: 59: Generated 10 of the 10 1-4 parameter combinations 59: 59: Excluding 2 bonded neighbours molecule type 'SOL' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.AllQuantumMol (30 ms) 59: [ RUN ] MimicTest.TwoQuantumMol 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 21.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 59: NVE simulation with an initial temperature of zero: will use a Verlet 59: buffer of 10%. Check your energy drift! 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 59: 59: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: NOTE: 20 % of the run time was spent in pair search, 59: you might want to increase nstlist (this has no effect on accuracy) 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.001 0.000 188.2 59: (ns/day) (hour/ns) 59: Performance: 205.087 0.117 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -554189393 59: 59: Generated 10 of the 10 non-bonded parameter combinations 59: 59: Generated 10 of the 10 1-4 parameter combinations 59: 59: Excluding 2 bonded neighbours molecule type 'SOL' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.TwoQuantumMol (27 ms) 59: [ RUN ] MimicTest.BondCuts 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 66.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 59: NVE simulation: will use the initial temperature of 300.368 K for 59: determining the Verlet buffer size 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/ala.gro' 59: 59: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: NOTE: 11 % of the run time was spent in pair search, 59: you might want to increase nstlist (this has no effect on accuracy) 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.002 0.001 194.3 59: (ns/day) (hour/ns) 59: Performance: 94.298 0.255 59: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2147446678 59: 59: Generated 2211 of the 2211 non-bonded parameter combinations 59: 59: Generated 2211 of the 2211 1-4 parameter combinations 59: 59: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 59: 59: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 59: 59: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 59: 59: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 59: 59: Note that mdrun will redetermine rlist based on the actual pair-list setup 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.BondCuts (73 ms) 59: [----------] 4 tests from MimicTest (159 ms total) 59: 59: [----------] 2 tests from WithIntegrator/ImdTest 59: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 59: Generating 1-4 interactions: fudge = 1 59: 59: NOTE 1 [file glycine_vacuo.top, line 12]: 59: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 59: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 59: the time step of 2.0e-03 ps. 59: Maybe you forgot to change the constraints mdp option. 59: 59: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 59: Number of degrees of freedom in T-Coupling group System is 27.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 2 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34 59: 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: IMD: Enabled. This simulation will accept incoming IMD connections. 59: IMD: Pulling from IMD remote is enabled (-imdpull). 59: IMD: Setting port for connection requests to 0. 59: IMD: Setting up incoming socket. 59: IMD: Listening for IMD connection on port 49161. 59: IMD: -imdwait not set, starting simulation. 59: starting mdrun 'Glycine' 59: 2 steps, 0.0 ps. 59: Setting the LD random seed to -16912390 59: 59: Generated 20503 of the 20503 non-bonded parameter combinations 59: 59: Generated 17396 of the 20503 1-4 parameter combinations 59: 59: Excluding 3 bonded neighbours molecule type 'Glycine' 59: 59: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 59: 59: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 59: 59: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm 59: 59: Note that mdrun will redetermine rlist based on the actual pair-list setup 59: 59: This run will generate roughly 0 Mb of data 59: 59: Writing final coordinates. 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.003 0.002 188.6 59: (ns/day) (hour/ns) 59: Performance: 327.311 0.073 59: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (399 ms) 59: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 59: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 59: apply to steep. 59: 59: Generating 1-4 interactions: fudge = 1 59: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 59: Number of degrees of freedom in T-Coupling group System is 27.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 2 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 59: Using 1 MPI thread 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: IMD: Enabled. This simulation will accept incoming IMD connections. 59: IMD: Pulling from IMD remote is enabled (-imdpull). 59: IMD: Setting port for connection requests to 0. 59: IMD: Setting up incoming socket. 59: IMD: Listening for IMD connection on port 50605. 59: IMD: -imdwait not set, starting simulation. 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = 1.19770464690297e+03 59: Maximum force = 1.77948604657896e+04 on atom 9 59: Norm of force = 7.87328617833980e+03 59: Setting the LD random seed to -951074841 59: 59: Generated 20503 of the 20503 non-bonded parameter combinations 59: 59: Generated 17396 of the 20503 1-4 parameter combinations 59: 59: Excluding 3 bonded neighbours molecule type 'Glycine' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (378 ms) 59: [----------] 2 tests from WithIntegrator/ImdTest (777 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 15 tests from 3 test suites ran. (1633 ms total) 59: [ PASSED ] 15 tests. 59/81 Test #59: MdrunModulesTests .............................. Passed 1.66 sec test 60 Start 60: MdrunIOTests 60: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 60: Test timeout computed to be: 600 60: [==========] Running 66 tests from 13 test suites. 60: [----------] Global test environment set-up. 60: [----------] 5 tests from GromppTest 60: [ RUN ] GromppTest.EmptyMdpFileWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Setting the LD random seed to -562495491 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.EmptyMdpFileWorks (17 ms) 60: [ RUN ] GromppTest.SimulatedAnnealingWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Simulated annealing for group rest: Periodic, 4 timepoints 60: Time (ps) Temperature (K) 60: 0.0 298.0 60: 2.0 320.0 60: 4.0 320.0 60: 6.0 298.0 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Setting the LD random seed to -65857 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.SimulatedAnnealingWorks (11 ms) 60: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Simulated annealing for group Methanol: Single, 3 timepoints 60: Time (ps) Temperature (K) 60: 0.0 298.0 60: 3.0 280.0 60: 6.0- 270.0 60: Simulated annealing for group SOL: Periodic, 4 timepoints 60: Time (ps) Temperature (K) 60: 0.0 298.0 60: 2.0 320.0 60: 4.0 320.0 60: 6.0 298.0 60: Number of degrees of freedom in T-Coupling group Methanol is 7.20 60: Number of degrees of freedom in T-Coupling group SOL is 4.80 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Setting the LD random seed to 2143213314 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (6 ms) 60: [ RUN ] GromppTest.ValidTransformationCoord 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Pull group 1 'SOL' has 3 atoms 60: Pull group 2 'Methanol' has 3 atoms 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 5 60: 2 3 2 0.613 nm 0.000 nm 60: 1 3 5 60: 2 3 2 0.613 nm 0.000 nm 60: 60: There were 3 notes 60: Setting the LD random seed to 2145901855 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.ValidTransformationCoord (36 ms) 60: [ RUN ] GromppTest.InvalidTransformationCoord 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Pull group 1 'SOL' has 3 atoms 60: Pull group 2 'Methanol' has 3 atoms 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 5 60: 2 3 2 0.613 nm 0.000 nm 60: 1 3 5 60: 2 3 2 Setting the LD random seed to -2013937738 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: [ OK ] GromppTest.InvalidTransformationCoord (23 ms) 60: [----------] 5 tests from GromppTest (96 ms total) 60: 60: [----------] 6 tests from MdrunTerminationTest 60: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -1093716420 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 198.3 60: (ns/day) (hour/ns) 60: Performance: 25.496 0.941 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 188.9 60: (ns/day) (hour/ns) 60: Performance: 288.602 0.083 60: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (42 ms) 60: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 1, rlist from 1.025 to 1 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 100 steps, 0.1 ps. 60: 60: Step 8: Run time exceeded 0.000 hours, will terminate the run within 2 steps 60: Setting the LD random seed to 525989739 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: NOTE: 11 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 189.4 60: (ns/day) (hour/ns) 60: Performance: 770.874 0.031 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Setting nsteps to 102 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 102 steps, 0.1 ps (continuing from step 9, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100 60: Runtime for the run 0.1 ps 60: Run end step 100 60: Run end time 0.1 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 102 60: Runtime for the run 0.102 ps 60: Run end step 102 60: Run end time 0.102 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.021 0.011 198.4 60: (ns/day) (hour/ns) 60: Performance: 761.523 0.032 60: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (41 ms) 60: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -830474245 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 188.2 60: (ns/day) (hour/ns) 60: Performance: 266.462 0.090 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 193.8 60: (ns/day) (hour/ns) 60: Performance: 265.875 0.090 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Setting nsteps to 6 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 6 60: Runtime for the run 0.006 ps 60: Run end step 6 60: Run end time 0.006 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 194.4 60: (ns/day) (hour/ns) 60: Performance: 287.381 0.084 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Setting nsteps to 8 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 6 60: Runtime for the run 0.006 ps 60: Run end step 6 60: Run end time 0.006 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 8 60: Runtime for the run 0.008 ps 60: Run end step 8 60: Run end time 0.008 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 192.8 60: (ns/day) (hour/ns) 60: Performance: 253.951 0.095 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: NOTE: 23 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.000 0.000 172.4 60: (ns/day) (hour/ns) 60: Performance: 450.171 0.053 60: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (52 ms) 60: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -470241805 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 189.4 60: (ns/day) (hour/ns) 60: Performance: 222.233 0.108 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps. 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 189.9 60: (ns/day) (hour/ns) 60: Performance: 399.546 0.060 60: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (24 ms) 60: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -303038603 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.012 0.006 197.0 60: (ns/day) (hour/ns) 60: Performance: 44.152 0.544 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Setting nsteps to 4 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (15 ms) 60: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -1831504401 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 190.2 60: (ns/day) (hour/ns) 60: Performance: 216.480 0.111 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 194.6 60: (ns/day) (hour/ns) 60: Performance: 212.503 0.113 60: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (20 ms) 60: [----------] 6 tests from MdrunTerminationTest (198 ms total) 60: 60: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 60: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.010 0.005 196.1 60: (ns/day) (hour/ns) 60: Performance: 292.567 0.082 60: trr version: GMX_trn_file (double precision) 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (18 ms) 60: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 198.8 60: (ns/day) (hour/ns) 60: Performance: 146.371 0.164 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (23 ms) 60: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (41 ms total) 60: 60: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.0 60: (ns/day) (hour/ns) 60: Performance: 921.141 0.026 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.019 0.009 198.4 60: (ns/day) (hour/ns) 60: Performance: 82.259 0.292 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.011 0.005 197.4 60: (ns/day) (hour/ns) 60: Performance: 142.554 0.168 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (77 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.012 0.006 198.4 60: (ns/day) (hour/ns) 60: Performance: 238.838 0.100 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.011 0.006 198.2 60: (ns/day) (hour/ns) 60: Performance: 137.442 0.175 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.018 0.009 198.1 60: (ns/day) (hour/ns) 60: Performance: 84.387 0.284 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (47 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 192.9 60: (ns/day) (hour/ns) 60: Performance: 1042.225 0.023 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.014 0.007 198.2 60: (ns/day) (hour/ns) 60: Performance: 112.137 0.214 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 191.1 60: (ns/day) (hour/ns) 60: Performance: 563.979 0.043 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (45 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 193.2 60: (ns/day) (hour/ns) 60: Performance: 1090.564 0.022 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 191.7 60: (ns/day) (hour/ns) 60: Performance: 602.084 0.040 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 192.7 60: (ns/day) (hour/ns) 60: Performance: 601.640 0.040 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (35 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 190.7 60: (ns/day) (hour/ns) 60: Performance: 990.290 0.024 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 190.4 60: (ns/day) (hour/ns) 60: Performance: 620.645 0.039 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 189.4 60: (ns/day) (hour/ns) 60: Performance: 551.860 0.043 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (35 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 196.9 60: (ns/day) (hour/ns) 60: Performance: 800.805 0.030 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 195.8 60: (ns/day) (hour/ns) 60: Performance: 513.782 0.047 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 194.4 60: (ns/day) (hour/ns) 60: Performance: 559.913 0.043 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (32 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 192.3 60: (ns/day) (hour/ns) 60: Performance: 1063.638 0.023 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 190.1 60: (ns/day) (hour/ns) 60: Performance: 625.526 0.038 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 191.2 60: (ns/day) (hour/ns) 60: Performance: 634.655 0.038 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (39 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 192.6 60: (ns/day) (hour/ns) 60: Performance: 971.856 0.025 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 25, rlist from 0.754 to 0.9 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 191.9 60: (ns/day) (hour/ns) 60: Performance: 618.292 0.039 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 25, rlist from 0.754 to 0.9 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 191.7 60: (ns/day) (hour/ns) 60: Performance: 570.989 0.042 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (35 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 193.6 60: (ns/day) (hour/ns) 60: Performance: 546.588 0.044 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.019 0.010 197.8 60: (ns/day) (hour/ns) 60: Performance: 78.879 0.304 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.4 60: (ns/day) (hour/ns) 60: Performance: 389.897 0.062 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (76 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 195.4 60: (ns/day) (hour/ns) 60: Performance: 458.753 0.052 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.4 60: (ns/day) (hour/ns) 60: Performance: 345.717 0.069 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 185.9 60: (ns/day) (hour/ns) 60: Performance: 366.213 0.066 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (68 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.022 0.011 198.4 60: (ns/day) (hour/ns) 60: Performance: 133.577 0.180 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: NOTE: 62 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.013 0.007 197.4 60: (ns/day) (hour/ns) 60: Performance: 116.753 0.206 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.013 0.006 197.3 60: (ns/day) (hour/ns) 60: Performance: 121.182 0.198 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (114 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.007 0.004 195.7 60: (ns/day) (hour/ns) 60: Performance: 412.135 0.058 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.014 0.007 197.7 60: (ns/day) (hour/ns) 60: Performance: 113.637 0.211 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.012 0.006 196.6 60: (ns/day) (hour/ns) 60: Performance: 123.682 0.194 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (102 ms) 60: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (713 ms total) 60: 60: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 192.9 60: (ns/day) (hour/ns) 60: Performance: 514.240 0.047 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.5 60: (ns/day) (hour/ns) 60: Performance: 331.049 0.072 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.021 0.011 198.0 60: (ns/day) (hour/ns) 60: Performance: 72.453 0.331 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (143 ms) 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: NOTE: 15 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.056 0.028 199.5 60: (ns/day) (hour/ns) 60: Performance: 51.890 0.463 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.030 0.015 199.1 60: (ns/day) (hour/ns) 60: Performance: 51.901 0.462 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: NOTE: 50 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.064 0.032 199.2 60: (ns/day) (hour/ns) 60: Performance: 24.246 0.990 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (207 ms) 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.025 0.013 197.6 60: (ns/day) (hour/ns) 60: Performance: 115.130 0.208 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.728 to 0.807 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 192.5 60: (ns/day) (hour/ns) 60: Performance: 244.270 0.098 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.728 to 0.807 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 193.4 60: (ns/day) (hour/ns) 60: Performance: 238.570 0.101 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (294 ms) 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.056 0.028 199.1 60: (ns/day) (hour/ns) 60: Performance: 52.304 0.459 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.023 0.012 197.9 60: (ns/day) (hour/ns) 60: Performance: 65.643 0.366 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.024 0.012 197.8 60: (ns/day) (hour/ns) 60: Performance: 64.851 0.370 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (320 ms) 60: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (965 ms total) 60: 60: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.8 60: (ns/day) (hour/ns) 60: Performance: 785.489 0.031 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.5 60: (ns/day) (hour/ns) 60: Performance: 499.922 0.048 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.8 60: (ns/day) (hour/ns) 60: Performance: 480.267 0.050 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (75 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.5 60: (ns/day) (hour/ns) 60: Performance: 756.923 0.032 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.2 60: (ns/day) (hour/ns) 60: Performance: 477.804 0.050 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.0 60: (ns/day) (hour/ns) 60: Performance: 446.535 0.054 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (60 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 190.8 60: (ns/day) (hour/ns) 60: Performance: 664.573 0.036 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.011 0.005 196.6 60: (ns/day) (hour/ns) 60: Performance: 142.772 0.168 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.0 60: (ns/day) (hour/ns) 60: Performance: 443.680 0.054 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (40 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 196.4 60: (ns/day) (hour/ns) 60: Performance: 495.344 0.048 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 195.9 60: (ns/day) (hour/ns) 60: Performance: 287.356 0.084 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.0 60: (ns/day) (hour/ns) 60: Performance: 360.386 0.067 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (37 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.007 0.004 197.2 60: (ns/day) (hour/ns) 60: Performance: 406.023 0.059 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 196.1 60: (ns/day) (hour/ns) 60: Performance: 293.934 0.082 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.007 0.003 193.9 60: (ns/day) (hour/ns) 60: Performance: 231.739 0.104 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (38 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.021 0.010 198.8 60: (ns/day) (hour/ns) 60: Performance: 141.770 0.169 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 196.4 60: (ns/day) (hour/ns) 60: Performance: 244.691 0.098 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.013 0.006 196.5 60: (ns/day) (hour/ns) 60: Performance: 121.702 0.197 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (50 ms) 60: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (301 ms total) 60: 60: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.3 60: (ns/day) (hour/ns) 60: Performance: 698.005 0.034 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.2 60: (ns/day) (hour/ns) 60: Performance: 483.470 0.050 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.1 60: (ns/day) (hour/ns) 60: Performance: 451.855 0.053 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (74 ms) 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.0 60: (ns/day) (hour/ns) 60: Performance: 731.054 0.033 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.7 60: (ns/day) (hour/ns) 60: Performance: 468.672 0.051 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.6 60: (ns/day) (hour/ns) 60: Performance: 438.608 0.055 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (96 ms) 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 196.4 60: (ns/day) (hour/ns) 60: Performance: 561.688 0.043 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.6 60: (ns/day) (hour/ns) 60: Performance: 343.459 0.070 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 193.4 60: (ns/day) (hour/ns) 60: Performance: 341.947 0.070 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (57 ms) 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 196.2 60: (ns/day) (hour/ns) 60: Performance: 541.781 0.044 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.1 60: (ns/day) (hour/ns) 60: Performance: 353.933 0.068 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 193.0 60: (ns/day) (hour/ns) 60: Performance: 339.916 0.071 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (48 ms) 60: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (277 ms total) 60: 60: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.8 60: (ns/day) (hour/ns) 60: Performance: 673.878 0.036 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 189.6 60: (ns/day) (hour/ns) 60: Performance: 419.053 0.057 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.1 60: (ns/day) (hour/ns) 60: Performance: 430.049 0.056 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (207 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.8 60: (ns/day) (hour/ns) 60: Performance: 719.611 0.033 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.7 60: (ns/day) (hour/ns) 60: Performance: 426.339 0.056 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.0 60: (ns/day) (hour/ns) 60: Performance: 444.042 0.054 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (95 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 189.5 60: (ns/day) (hour/ns) 60: Performance: 706.166 0.034 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.0 60: (ns/day) (hour/ns) 60: Performance: 445.194 0.054 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.7 60: (ns/day) (hour/ns) 60: Performance: 444.708 0.054 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (96 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.8 60: (ns/day) (hour/ns) 60: Performance: 634.263 0.038 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.6 60: (ns/day) (hour/ns) 60: Performance: 451.542 0.053 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 190.9 60: (ns/day) (hour/ns) 60: Performance: 421.763 0.057 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (71 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.006 65.5 60: (ns/day) (hour/ns) 60: Performance: 229.189 0.105 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.019 0.010 197.1 60: (ns/day) (hour/ns) 60: Performance: 80.056 0.300 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.012 0.006 196.7 60: (ns/day) (hour/ns) 60: Performance: 127.372 0.188 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (43 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.034 0.017 198.6 60: (ns/day) (hour/ns) 60: Performance: 85.080 0.282 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.010 0.005 196.0 60: (ns/day) (hour/ns) 60: Performance: 159.853 0.150 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.010 0.005 195.8 60: (ns/day) (hour/ns) 60: Performance: 156.067 0.154 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (50 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.0 60: (ns/day) (hour/ns) 60: Performance: 725.373 0.033 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 197.9 60: (ns/day) (hour/ns) 60: Performance: 75.278 0.319 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 188.8 60: (ns/day) (hour/ns) 60: Performance: 433.940 0.055 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (73 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.021 0.011 198.2 60: (ns/day) (hour/ns) 60: Performance: 137.901 0.174 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.2 60: (ns/day) (hour/ns) 60: Performance: 466.527 0.051 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.066 0.033 199.2 60: (ns/day) (hour/ns) 60: Performance: 23.581 1.018 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (86 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.3 60: (ns/day) (hour/ns) 60: Performance: 650.607 0.037 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.8 60: (ns/day) (hour/ns) 60: Performance: 474.468 0.051 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.1 60: (ns/day) (hour/ns) 60: Performance: 422.637 0.057 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (69 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.032 0.016 199.2 60: (ns/day) (hour/ns) 60: Performance: 90.008 0.267 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 195.8 60: (ns/day) (hour/ns) 60: Performance: 261.820 0.092 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.0 60: (ns/day) (hour/ns) 60: Performance: 337.489 0.071 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (89 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.024 0.012 198.9 60: (ns/day) (hour/ns) 60: Performance: 122.621 0.196 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 198.0 60: (ns/day) (hour/ns) 60: Performance: 75.694 0.317 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.8 60: (ns/day) (hour/ns) 60: Performance: 337.733 0.071 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (75 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.014 0.007 198.4 60: (ns/day) (hour/ns) 60: Performance: 205.511 0.117 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.003 154.6 60: (ns/day) (hour/ns) 60: Performance: 269.678 0.089 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.7 60: (ns/day) (hour/ns) 60: Performance: 333.349 0.072 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (72 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 1.617 0.809 200.0 60: (ns/day) (hour/ns) 60: Performance: 1.816 13.216 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 195.4 60: (ns/day) (hour/ns) 60: Performance: 301.627 0.080 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 191.3 60: (ns/day) (hour/ns) 60: Performance: 326.214 0.074 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (886 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 177.2 60: (ns/day) (hour/ns) 60: Performance: 482.692 0.050 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.3 60: (ns/day) (hour/ns) 60: Performance: 384.157 0.062 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 191.8 60: (ns/day) (hour/ns) 60: Performance: 306.243 0.078 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (38 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.008 0.004 196.9 60: (ns/day) (hour/ns) 60: Performance: 370.562 0.065 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 194.7 60: (ns/day) (hour/ns) 60: Performance: 349.383 0.069 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 197.8 60: (ns/day) (hour/ns) 60: Performance: 75.302 0.319 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (45 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 60: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (0 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 60: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (0 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.030 0.015 199.1 60: (ns/day) (hour/ns) 60: Performance: 97.989 0.245 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.013 0.007 197.7 60: (ns/day) (hour/ns) 60: Performance: 119.320 0.201 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 190.3 60: (ns/day) (hour/ns) 60: Performance: 292.510 0.082 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (50 ms) 60: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (2053 ms total) 60: 60: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 60: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.024 0.012 199.0 60: (ns/day) (hour/ns) 60: Performance: 124.160 0.193 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 195.5 60: (ns/day) (hour/ns) 60: Performance: 331.520 0.072 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 192.6 60: (ns/day) (hour/ns) 60: Performance: 314.694 0.076 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (62 ms) 60: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (63 ms total) 60: 60: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 60: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.3 60: (ns/day) (hour/ns) 60: Performance: 853.268 0.028 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 189.9 60: (ns/day) (hour/ns) 60: Performance: 532.228 0.045 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 189.9 60: (ns/day) (hour/ns) 60: Performance: 537.048 0.045 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (84 ms) 60: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 195.8 60: (ns/day) (hour/ns) 60: Performance: 624.427 0.038 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.4 60: (ns/day) (hour/ns) 60: Performance: 386.845 0.062 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.8 60: (ns/day) (hour/ns) 60: Performance: 382.984 0.063 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (99 ms) 60: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (183 ms total) 60: 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: Setting the AWH bias MC random seed to -1664113795 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Setting the AWH bias MC random seed to -222325459 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.069 0.034 198.9 60: (ns/day) (hour/ns) 60: Performance: 42.611 0.563 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 25, rlist from 0.748 to 0.878 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 191.6 60: (ns/day) (hour/ns) 60: Performance: 264.367 0.091 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 25, rlist from 0.748 to 0.878 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 189.7 60: (ns/day) (hour/ns) 60: Performance: 282.087 0.085 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (220 ms) 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: Setting the AWH bias MC random seed to 1063256025 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Setting the AWH bias MC random seed to -578446465 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.127 0.064 199.6 60: (ns/day) (hour/ns) 60: Performance: 23.019 1.043 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 25, rlist from 0.748 to 0.878 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.035 0.018 197.7 60: (ns/day) (hour/ns) 60: Performance: 44.408 0.540 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 25, rlist from 0.748 to 0.878 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 191.5 60: (ns/day) (hour/ns) 60: Performance: 267.357 0.090 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (256 ms) 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (477 ms total) 60: 60: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 60: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: NOTE: 33 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.055 0.027 199.5 60: (ns/day) (hour/ns) 60: Performance: 53.697 0.447 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.050 0.025 199.3 60: (ns/day) (hour/ns) 60: Performance: 31.066 0.773 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 60: 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.038 0.019 198.1 60: (ns/day) (hour/ns) 60: Performance: 40.836 0.588 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (234 ms) 60: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (235 ms total) 60: 60: [----------] 3 tests from Checking/InitialConstraintsTest 60: [ RUN ] Checking/InitialConstraintsTest.Works/0 60: Number of degrees of freedom in T-Coupling group rest is 11.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 1141.954 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc-and-methanol' 60: 1 steps, 0.0 ps. 60: Setting the LD random seed to -268895442 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 186.4 60: (ns/day) (hour/ns) 60: Performance: 131.443 0.183 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (30 ms) 60: [ RUN ] Checking/InitialConstraintsTest.Works/1 60: Number of degrees of freedom in T-Coupling group rest is 11.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 1141.954 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc-and-methanol' 60: 1 steps, 0.0 ps. 60: Setting the LD random seed to -1166540826 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.035 0.018 199.1 60: (ns/day) (hour/ns) 60: Performance: 9.704 2.473 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (34 ms) 60: [ RUN ] Checking/InitialConstraintsTest.Works/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 60: Integrator method md-vv-avek is implemented primarily for validation 60: purposes; for molecular dynamics, you should probably be using md or md-vv 60: 60: Number of degrees of freedom in T-Coupling group rest is 11.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 60: NVE simulation: will use the initial temperature of 1141.954 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI thread 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc-and-methanol' 60: 1 steps, 0.0 ps. 60: Setting the LD random seed to -537923625 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 186.8 60: (ns/day) (hour/ns) 60: Performance: 126.290 0.190 60: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (37 ms) 60: [----------] 3 tests from Checking/InitialConstraintsTest (102 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 66 tests from 13 test suites ran. (7676 ms total) 60: [ PASSED ] 66 tests. 60/81 Test #60: MdrunIOTests ................................... Passed 7.75 sec test 61 Start 61: MdrunTestsOneRank 61: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunTestsOneRank.xml" 61: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 61: Test timeout computed to be: 600 61: [==========] Running 22 tests from 6 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from CompelTest 61: [ RUN ] CompelTest.SwapCanRun 61: Generating 1-4 interactions: fudge = 0.5 61: Split0 group 'Ch0' contains 83 atoms. 61: Split1 group 'Ch1' contains 83 atoms. 61: Solvent group 'SOL' contains 11931 atoms. 61: Swap group 'NA+' contains 19 atoms. 61: Swap group 'CL-' contains 19 atoms. 61: Number of degrees of freedom in T-Coupling group System is 27869.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 61: Removing center of mass motion in the presence of position restraints 61: might cause artifacts. When you are using position restraints to 61: equilibrate a macro-molecule, the artifacts are usually negligible. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: SWAP: Determining initial numbers of ions per compartment. 61: SWAP: Setting pointers for checkpoint writing 61: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 61: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 61: starting mdrun 'Channel_coco in octane membrane' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to 1341808061 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein' 61: 61: turning all bonds into constraints... 61: 61: Excluding 3 bonded neighbours molecule type 'OCT' 61: 61: turning all bonds into constraints... 61: 61: Excluding 1 bonded neighbours molecule type 'NA' 61: 61: turning all bonds into constraints... 61: 61: Excluding 1 bonded neighbours molecule type 'CL' 61: 61: turning all bonds into constraints... 61: 61: Excluding 3 bonded neighbours molecule type 'Protein' 61: 61: Excluding 3 bonded neighbours molecule type 'OCT' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: turning all bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 1 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 44 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 1.269 0.634 200.0 61: (ns/day) (hour/ns) 61: Performance: 2.043 11.749 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: SWAP: Setting pointers for checkpoint writing 61: SWAP: Copying channel fluxes from checkpoint file data 61: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 61: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 61: starting mdrun 'Channel_coco in octane membrane' 61: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 61: 61: Writing final coordinates. 61: 61: NOTE: 28 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.899 0.450 199.9 61: (ns/day) (hour/ns) 61: Performance: 2.883 8.324 61: [ OK ] CompelTest.SwapCanRun (2642 ms) 61: [----------] 1 test from CompelTest (2642 ms total) 61: 61: [----------] 6 tests from BondedInteractionsTest 61: [ RUN ] BondedInteractionsTest.NormalBondWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 2 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 16 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 188.1 61: (ns/day) (hour/ns) 61: Performance: 233.648 0.103 61: Setting the LD random seed to -23078669 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.NormalBondWorks (25 ms) 61: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 2 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 18 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 187.0 61: (ns/day) (hour/ns) 61: Performance: 242.238 0.099 61: Setting the LD random seed to -33834245 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.TabulatedBondWorks (35 ms) 61: [ RUN ] BondedInteractionsTest.NormalAngleWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 18 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 187.5 61: (ns/day) (hour/ns) 61: Performance: 261.086 0.092 61: Setting the LD random seed to -201622577 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.NormalAngleWorks (23 ms) 61: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 18 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 188.4 61: (ns/day) (hour/ns) 61: Performance: 232.897 0.103 61: Setting the LD random seed to -8668195 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (12 ms) 61: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 20 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 188.4 61: (ns/day) (hour/ns) 61: Performance: 246.690 0.097 61: Setting the LD random seed to -101720330 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.NormalDihedralWorks (8 ms) 61: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 19 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.000 188.2 61: (ns/day) (hour/ns) 61: Performance: 278.760 0.086 61: Setting the LD random seed to -84606994 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (12 ms) 61: [----------] 6 tests from BondedInteractionsTest (118 ms total) 61: 61: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to 1404893119 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.094 0.047 199.4 61: (ns/day) (hour/ns) 61: Performance: 9.185 2.613 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to -1140998228 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.094 0.047 199.2 61: (ns/day) (hour/ns) 61: Performance: 9.175 2.616 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 61: 61: 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (1082 ms) 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to 2145120059 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.042 0.021 198.7 61: (ns/day) (hour/ns) 61: Performance: 20.563 1.167 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 61: Can not increase nstlist because an NVE ensemble is used 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to -8193 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.032 0.016 198.4 61: (ns/day) (hour/ns) 61: Performance: 26.982 0.889 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 61: 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (246 ms) 61: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (1329 ms total) 61: 61: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 61: Generating 1-4 interactions: fudge = 0.5 61: Pull group 1 'FirstWaterMolecule' has 3 atoms 61: Pull group 2 'SecondWaterMolecule' has 3 atoms 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: Pull group natoms pbc atom distance at start reference at t=0 61: 1 3 2 61: 2 3 5 1.112 nm 1.000 nm 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to 2126511930 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: turning H bonds into constraints... 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.025 0.013 197.7 61: (ns/day) (hour/ns) 61: Performance: 33.607 0.714 61: Generating 1-4 interactions: fudge = 0.5 61: Pull group 1 'FirstWaterMolecule' has 3 atoms 61: Pull group 2 'SecondWaterMolecule' has 3 atoms 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: Pull group natoms pbc atom distance at start reference at t=0 61: 1 3 2 61: 2 3 5 1.112 nm 1.000 nm 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 61: Can not increase nstlist because an NVE ensemble is used 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 4 steps, 0.0 ps. 61: Setting the LD random seed to -2429153 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: turning H bonds into constraints... 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.003 0.002 189.7 61: (ns/day) (hour/ns) 61: Performance: 249.201 0.096 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 61: 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (69 ms) 61: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (69 ms total) 61: 61: [----------] 8 tests from FreezeWorks/FreezeGroupTest 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: NVE simulation: will use the initial temperature of 318.937 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 5 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.044 0.022 198.8 61: (ns/day) (hour/ns) 61: Performance: 34.888 0.688 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (85 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: NVE simulation: will use the initial temperature of 318.937 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 5 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.004 0.002 189.1 61: (ns/day) (hour/ns) 61: Performance: 363.762 0.066 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (66 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: NVE simulation: will use the initial temperature of 318.937 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 5 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.021 0.011 198.1 61: (ns/day) (hour/ns) 61: Performance: 71.925 0.334 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (59 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 61: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 61: Parrinello-Rahman is not implemented in md-vv. 61: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (0 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Changing nstlist from 8 to 25, rlist from 0.748 to 0.878 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.004 0.002 191.7 61: (ns/day) (hour/ns) 61: Performance: 347.596 0.069 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (49 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Changing nstlist from 8 to 25, rlist from 0.748 to 0.878 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.006 0.003 193.2 61: (ns/day) (hour/ns) 61: Performance: 268.060 0.090 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (29 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.005 0.002 192.1 61: (ns/day) (hour/ns) 61: Performance: 324.526 0.074 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (38 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.006 0.003 192.5 61: (ns/day) (hour/ns) 61: Performance: 247.420 0.097 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (36 ms) 61: [----------] 8 tests from FreezeWorks/FreezeGroupTest (366 ms total) 61: 61: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to 2012165717 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.003 0.002 188.9 61: (ns/day) (hour/ns) 61: Performance: 895.276 0.027 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (56 ms) 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because verlet-buffer-tolerance is not set or used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to 983548525 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.003 0.002 189.2 61: (ns/day) (hour/ns) 61: Performance: 915.892 0.026 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (52 ms) 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to -1075986577 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.004 0.002 189.7 61: (ns/day) (hour/ns) 61: Performance: 826.950 0.029 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (33 ms) 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 61: Can not increase nstlist because verlet-buffer-tolerance is not set or used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to -671088798 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.004 0.002 189.8 61: (ns/day) (hour/ns) 61: Performance: 821.948 0.029 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (15 ms) 61: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (157 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 22 tests from 6 test suites ran. (5642 ms total) 61: [ PASSED ] 21 tests. 61: [ SKIPPED ] 1 test, listed below: 61: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 61/81 Test #61: MdrunTestsOneRank .............................. Passed 5.73 sec test 62 Start 62: MdrunTestsTwoRanks 62: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunTestsTwoRanks.xml" 62: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 62: Test timeout computed to be: 600 62: [==========] Running 22 tests from 6 test suites. 62: [----------] Global test environment set-up. 62: [----------] 1 test from CompelTest 62: [ RUN ] CompelTest.SwapCanRun 62: Generating 1-4 interactions: fudge = 0.5 62: Split0 group 'Ch0' contains 83 atoms. 62: Split1 group 'Ch1' contains 83 atoms. 62: Solvent group 'SOL' contains 11931 atoms. 62: Swap group 'NA+' contains 19 atoms. 62: Swap group 'CL-' contains 19 atoms. 62: Number of degrees of freedom in T-Coupling group System is 27869.00 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 62: Removing center of mass motion in the presence of position restraints 62: might cause artifacts. When you are using position restraints to 62: equilibrate a macro-molecule, the artifacts are usually negligible. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: SWAP: Determining initial numbers of ions per compartment. 62: SWAP: Setting pointers for checkpoint writing 62: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 62: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 62: starting mdrun 'Channel_coco in octane membrane' 62: 2 steps, 0.0 ps. 62: Setting the LD random seed to 1055913917 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein' 62: 62: turning all bonds into constraints... 62: 62: Excluding 3 bonded neighbours molecule type 'OCT' 62: 62: turning all bonds into constraints... 62: 62: Excluding 1 bonded neighbours molecule type 'NA' 62: 62: turning all bonds into constraints... 62: 62: Excluding 1 bonded neighbours molecule type 'CL' 62: 62: turning all bonds into constraints... 62: 62: Excluding 3 bonded neighbours molecule type 'Protein' 62: 62: Excluding 3 bonded neighbours molecule type 'OCT' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: turning all bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 1 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 7.0%. 62: The balanceable part of the MD step is 13%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.9%. 62: 62: 62: NOTE: 12 % of the run time was spent in domain decomposition, 62: 31 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 2.462 0.616 399.9 62: (ns/day) (hour/ns) 62: Performance: 2.105 11.400 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: SWAP: Setting pointers for checkpoint writing 62: SWAP: Copying channel fluxes from checkpoint file data 62: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 62: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 62: starting mdrun 'Channel_coco in octane membrane' 62: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 62: 62: Writing final coordinates. 62: 62: NOTE: 17 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 1.701 0.425 399.8 62: (ns/day) (hour/ns) 62: Performance: 3.046 7.879 62: [ OK ] CompelTest.SwapCanRun (2239 ms) 62: [----------] 1 test from CompelTest (2239 ms total) 62: 62: [----------] 6 tests from BondedInteractionsTest 62: [ RUN ] BondedInteractionsTest.NormalBondWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 2 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 22 % of the run time was spent in domain decomposition, 62: 9 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.002 0.001 377.9 62: (ns/day) (hour/ns) 62: Performance: 142.252 0.169 62: Setting the LD random seed to 653786622 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.NormalBondWorks (121 ms) 62: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 2 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.018 0.004 396.4 62: (ns/day) (hour/ns) 62: Performance: 19.486 1.232 62: Setting the LD random seed to -6332931 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.TabulatedBondWorks (100 ms) 62: [ RUN ] BondedInteractionsTest.NormalAngleWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 65 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 9 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.176 0.044 399.5 62: (ns/day) (hour/ns) 62: Performance: 1.958 12.259 62: Setting the LD random seed to 1592594425 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.NormalAngleWorks (113 ms) 62: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 60 % of the run time was spent in domain decomposition, 62: 4 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 6 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.412 0.103 399.8 62: (ns/day) (hour/ns) 62: Performance: 0.839 28.614 62: Setting the LD random seed to -4328497 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (224 ms) 62: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 29 % of the run time was spent in domain decomposition, 62: 1 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.058 0.015 398.9 62: (ns/day) (hour/ns) 62: Performance: 5.935 4.044 62: Setting the LD random seed to -876619270 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.NormalDihedralWorks (109 ms) 62: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: 62: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 16 % of the run time was spent in domain decomposition, 62: 10 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.002 0.001 380.3 62: (ns/day) (hour/ns) 62: Performance: 136.673 0.176 62: Setting the LD random seed to -582230827 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (76 ms) 62: [----------] 6 tests from BondedInteractionsTest (747 ms total) 62: 62: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 62: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to -270714969 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 43 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.096 0.024 397.0 62: (ns/day) (hour/ns) 62: Performance: 17.844 1.345 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to -3165190 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 17 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.156 0.039 398.4 62: (ns/day) (hour/ns) 62: Performance: 11.011 2.180 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 62: 62: 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (1309 ms) 62: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to -338822273 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 11 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 6 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 2.168 0.551 393.8 62: (ns/day) (hour/ns) 62: Performance: 0.785 30.586 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 62: Can not increase nstlist because an NVE ensemble is used 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to -1276118852 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 20 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.015 0.004 383.1 62: (ns/day) (hour/ns) 62: Performance: 110.276 0.218 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 62: 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (1064 ms) 62: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (2373 ms total) 62: 62: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 62: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 62: Generating 1-4 interactions: fudge = 0.5 62: Pull group 1 'FirstWaterMolecule' has 3 atoms 62: Pull group 2 'SecondWaterMolecule' has 3 atoms 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: Pull group natoms pbc atom distance at start reference at t=0 62: 1 3 2 62: 2 3 5 1.112 nm 1.000 nm 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to -33827073 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: turning H bonds into constraints... 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 95 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.193 0.048 399.0 62: (ns/day) (hour/ns) 62: Performance: 8.927 2.688 62: Generating 1-4 interactions: fudge = 0.5 62: Pull group 1 'FirstWaterMolecule' has 3 atoms 62: Pull group 2 'SecondWaterMolecule' has 3 atoms 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: Pull group natoms pbc atom distance at start reference at t=0 62: 1 3 2 62: 2 3 5 1.112 nm 1.000 nm 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 62: Can not increase nstlist because an NVE ensemble is used 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 4 steps, 0.0 ps. 62: Setting the LD random seed to -604516485 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: turning H bonds into constraints... 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 35 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.009 0.002 374.6 62: (ns/day) (hour/ns) 62: Performance: 187.358 0.128 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 62: 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (317 ms) 62: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (317 ms total) 62: 62: [----------] 8 tests from FreezeWorks/FreezeGroupTest 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: NVE simulation: will use the initial temperature of 318.937 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 27.1%. 62: The balanceable part of the MD step is 1%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.2%. 62: 62: 62: NOTE: 47 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 32 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.394 0.102 385.0 62: (ns/day) (hour/ns) 62: Performance: 7.606 3.155 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (328 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: NVE simulation: will use the initial temperature of 318.937 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 14.4%. 62: The balanceable part of the MD step is 1%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.1%. 62: 62: 62: NOTE: 49 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.378 0.095 399.4 62: (ns/day) (hour/ns) 62: Performance: 8.219 2.920 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (327 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: NVE simulation: will use the initial temperature of 318.937 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 15.0%. 62: The balanceable part of the MD step is 2%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.3%. 62: 62: 62: NOTE: 94 % of the run time was spent in domain decomposition, 62: 0 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.172 0.043 398.7 62: (ns/day) (hour/ns) 62: Performance: 17.999 1.333 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (260 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 62: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 62: Parrinello-Rahman is not implemented in md-vv. 62: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (0 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Changing nstlist from 8 to 25, rlist from 0.748 to 0.878 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 25 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.011 0.003 382.6 62: (ns/day) (hour/ns) 62: Performance: 262.621 0.091 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (240 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Changing nstlist from 8 to 25, rlist from 0.748 to 0.878 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 26 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.010 0.003 384.1 62: (ns/day) (hour/ns) 62: Performance: 310.013 0.077 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (200 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.106 0.027 398.4 62: (ns/day) (hour/ns) 62: Performance: 29.128 0.824 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (141 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 62: 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 39 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.050 0.024 206.6 62: (ns/day) (hour/ns) 62: Performance: 32.218 0.745 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (172 ms) 62: [----------] 8 tests from FreezeWorks/FreezeGroupTest (1672 ms total) 62: 62: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to -555991178 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 20.6%. 62: The balanceable part of the MD step is 37%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 7.7%. 62: 62: NOTE: 7.7 % of the available CPU time was lost due to load imbalance 62: in the domain decomposition. 62: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 62: You can also consider manually changing the decomposition (option -dd); 62: e.g. by using fewer domains along the box dimension in which there is 62: considerable inhomogeneity in the simulated system. 62: 62: NOTE: 15 % of the run time was spent in domain decomposition, 62: 4 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 24 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.009 0.002 380.9 62: (ns/day) (hour/ns) 62: Performance: 648.956 0.037 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (107 ms) 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because verlet-buffer-tolerance is not set or used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to -688954433 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 11.9%. 62: The balanceable part of the MD step is 5%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.6%. 62: 62: 62: NOTE: 77 % of the run time was spent in domain decomposition, 62: 1 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 7 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.039 0.010 393.8 62: (ns/day) (hour/ns) 62: Performance: 156.490 0.153 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (128 ms) 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to 918515688 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 2.7%. 62: The balanceable part of the MD step is 48%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 1.3%. 62: 62: 62: NOTE: 12 % of the run time was spent in domain decomposition, 62: 5 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 26 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.008 0.002 376.4 62: (ns/day) (hour/ns) 62: Performance: 715.161 0.034 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (94 ms) 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 62: Can not increase nstlist because verlet-buffer-tolerance is not set or used 62: Using 2 MPI threads 62: Using 2 OpenMP threads per tMPI thread 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to -19007638 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 2.2%. 62: The balanceable part of the MD step is 53%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 1.2%. 62: 62: 62: NOTE: 11 % of the run time was spent in domain decomposition, 62: 4 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 24 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.007 0.002 379.9 62: (ns/day) (hour/ns) 62: Performance: 834.942 0.029 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (41 ms) 62: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (372 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 22 tests from 6 test suites ran. (8669 ms total) 62: [ PASSED ] 21 tests. 62: [ SKIPPED ] 1 test, listed below: 62: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 62/81 Test #62: MdrunTestsTwoRanks ............................. Passed 8.73 sec test 63 Start 63: MdrunSingleRankAlgorithmsTests 63: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 63: Test timeout computed to be: 600 63: [==========] Running 4 tests from 2 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from OriresTest 63: [ RUN ] OriresTest.OriresCanRun 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 518.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 note 63: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 63: log). 63: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 63: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 63: Changing nstlist from 10 to 25, rlist from 1.059 to 1.178 63: 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 63: 10 steps, 0.0 ps. 63: Setting the LD random seed to 1442535391 63: 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.096 0.048 199.5 63: (ns/day) (hour/ns) 63: Performance: 39.577 0.606 63: [ OK ] OriresTest.OriresCanRun (733 ms) 63: [----------] 1 test from OriresTest (733 ms total) 63: 63: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 63: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 63: Number of degrees of freedom in T-Coupling group rest is 10.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 63: The optimal PME mesh load for parallel simulations is below 0.5 63: and for highly parallel simulations between 0.25 and 0.33, 63: for higher performance, increase the cut-off and the PME grid spacing. 63: 63: 63: 63: There were 2 notes 63: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 63: log). 63: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Dipoles' 63: 20 steps, 0.1 ps. 63: Setting the LD random seed to -6512642 63: 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Dipole' 63: 63: Searching the wall atom type(s) 63: 63: The largest distance between excluded atoms is 0.344 nm 63: Calculating fourier grid dimensions for X Y Z 63: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 63: 63: Estimate for the relative computational load of the PME mesh part: 1.00 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.154 0.077 199.7 63: (ns/day) (hour/ns) 63: Performance: 58.742 0.409 63: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision) 63: 63: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (1472 ms) 63: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 63: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 63: The supported numbers are > 1. 63: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 63: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: With epsilon_surface > 0 all molecules should be neutral. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: With epsilon_surface > 0 you can only use domain decomposition when there 63: are only small molecules with all bonds constrained (mdrun will check for 63: this). 63: 63: Number of degrees of freedom in T-Coupling group rest is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: The optimal PME mesh load for parallel simulations is below 0.5 63: and for highly parallel simulations between 0.25 and 0.33, 63: for higher performance, increase the cut-off and the PME grid spacing. 63: 63: 63: 63: There were 4 notes 63: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 63: log). 63: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Dipoles' 63: 20 steps, 0.1 ps. 63: Setting the LD random seed to -1073748002 63: 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Dipole' 63: 63: The largest distance between excluded atoms is 0.344 nm 63: Calculating fourier grid dimensions for X Y Z 63: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 63: 63: Estimate for the relative computational load of the PME mesh part: 1.00 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.047 0.023 198.9 63: (ns/day) (hour/ns) 63: Performance: 193.834 0.124 63: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 63: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (520 ms) 63: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (1993 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 4 tests from 2 test suites ran. (3006 ms total) 63: [ PASSED ] 4 tests. 63/81 Test #63: MdrunSingleRankAlgorithmsTests ................. Passed 3.03 sec test 64 Start 64: MdrunNonIntegratorTests 64: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 65 tests from 7 test suites. 64: [----------] Global test environment set-up. 64: [----------] 1 test from NonbondedBenchTest 64: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 64: SIMD width: 2 64: System size: 3000 atoms 64: Cut-off radius: 1 nm 64: Number of threads: 1 64: Number of iterations: 1 64: Compute energies: no 64: Ewald excl. corr.: analytical 64: 64: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 64: total useful 64: Ewald all geom. 4xM 55.433 55.4329 0.0191 0.0114 64: [ OK ] NonbondedBenchTest.BasicEndToEndTest (69 ms) 64: [----------] 1 test from NonbondedBenchTest (69 ms total) 64: 64: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -4.79910463671055e+01 64: Maximum force = 1.86297359432216e+02 on atom 13 64: Norm of force = 8.77219865482116e+01 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1093 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 3.02331e+02 on atom 3 64: F-Norm = 1.18024e+02 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -5.58622538633291e+01 64: Maximum force = 4.27274822366516e+02 on atom 13 64: Norm of force = 1.84530029253834e+02 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1312 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 22.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 3.19376899751522e+02 64: Maximum force = 9.99884921009767e+03 on atom 9 64: Norm of force = 4.61669565054298e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (335 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: 64: NOTE 3 [file glycine_vacuo.top, line 12]: 64: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 64: 64: Number of degrees of freedom in T-Coupling group System is 22.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 2.41575e+04 on atom 10 64: F-Norm = 1.18451e+04 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 1.51743018140927e+02 64: Maximum force = 7.42089573409110e+03 on atom 9 64: Norm of force = 3.56929298615738e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (332 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -1.56984193848274e+02 64: Maximum force = 4.56923624626478e+02 on atom 17 64: Norm of force = 1.83258377168370e+02 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (64 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: 64: NOTE 4 [file unknown]: 64: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 1.06800e+03 on atom 28 64: F-Norm = 4.26922e+02 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -1.69410778678186e+02 64: Maximum force = 2.18225948474111e+02 on atom 17 64: Norm of force = 7.92068036537837e+01 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (48 ms) 64: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (3187 ms total) 64: 64: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents converged to Fmax < 10 in 1 steps 64: Potential Energy = -9.74257075835447e-01 64: Maximum force = 4.01322929015133e+00 on atom 1 64: Norm of force = 1.63839399694378e+00 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (29 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 4.01323e+00 on atom 1 64: F-Norm = 1.63839e+00 64: 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 64: Potential Energy = -9.90642313893969e-01 64: Maximum force = 2.57812909490791e+00 on atom 1 64: Norm of force = 1.05251679559130e+00 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (9 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: 64: There was 1 warning 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Low-Memory BFGS Minimizer: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: Using 10 BFGS correction steps. 64: 64: F-max = 4.01323e+00 on atom 1 64: F-Norm = 1.63839e+00 64: 64: 64: writing lowest energy coordinates. 64: 64: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 64: Potential Energy = -9.90642313893969e-01 64: Maximum force = 2.57812909490791e+00 on atom 1 64: Norm of force = 1.05251679559130e+00 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (13 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 3.19395484891518e+02 64: Maximum force = 9.97041707197910e+03 on atom 9 64: Norm of force = 4.62274878665467e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (161 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 2.41672e+04 on atom 10 64: F-Norm = 1.19357e+04 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 1.56258793899480e+02 64: Maximum force = 7.50181017480396e+03 on atom 9 64: Norm of force = 3.61390332564874e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (181 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: 64: There was 1 warning 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Low-Memory BFGS Minimizer: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: Using 10 BFGS correction steps. 64: 64: F-max = 2.41672e+04 on atom 10 64: F-Norm = 1.19357e+04 64: 64: 64: Energy minimization has stopped, but the forces have not converged to the 64: requested precision Fmax < 10 (which may not be possible for your system). It 64: stopped because the algorithm tried to make a new step whose size was too 64: small, or there was no change in the energy since last step. Either way, we 64: regard the minimization as converged to within the available machine 64: precision, given your starting configuration and EM parameters. 64: 64: writing lowest energy coordinates. 64: 64: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 64: but did not reach the requested Fmax < 10. 64: Potential Energy = 5.61116097794204e+02 64: Maximum force = 1.26854826291223e+04 on atom 10 64: Norm of force = 6.06436286976271e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (182 ms) 64: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (577 ms total) 64: 64: [----------] 5 tests from NormalModesWorks/NormalModesTest 64: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 15.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Small system size (N=6), using full Hessian format. 64: Allocating Hessian memory... 64: 64: starting normal mode calculation '2 scaled waters' 64: 12 steps. 64: 64: Maximum force: 9.96989e-06 64: 64: 64: Writing Hessian... 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Reading double precision matrix generated by GROMACS 2022.5-Debian_2022.5_2 64: 64: Diagonalizing to find vectors 7 through 18... 64: Writing eigenvalues... 64: 64: Writing average structure & eigenvectors 7--18 to eigenvec.trr 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: There are: 6 Atoms 64: Using begin = 7 and end = 18 64: Full matrix storage format, nrow=18, ncols=18 64: Writing eigenfrequencies - negative eigenvalues will be set to zero. 64: Cannot compute entropy when -first = 7 64: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (187 ms) 64: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: 64: NOTE 3 [file villin.top, line 2452]: 64: System has non-zero total charge: -2.000000 64: Total charge should normally be an integer. See 64: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 64: for discussion on how close it should be to an integer. 64: 64: 64: 64: Number of degrees of freedom in T-Coupling group System is 765.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Small system size (N=256), using full Hessian format. 64: Allocating Hessian memory... 64: 64: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 64: 512 steps. 64: 64: Maximum force: 6.97568e-04 64: 64: 64: Writing Hessian... 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Reading double precision matrix generated by GROMACS 2022.5-Debian_2022.5_2 64: 64: Diagonalizing to find vectors 7 through 50... 64: Writing eigenvalues... 64: 64: Writing average structure & eigenvectors 7--50 to eigenvec.trr 64: Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: This run will generate roughly 0 Mb of data 64: There are: 256 Atoms 64: Using begin = 7 and end = 50 64: Full matrix storage format, nrow=768, ncols=768 64: Writing eigenfrequencies - negative eigenvalues will be set to zero. 64: Cannot compute entropy when -first = 7 64: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (4975 ms) 64: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 15.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Small system size (N=6), using full Hessian format. 64: Allocating Hessian memory... 64: 64: starting normal mode calculation 'flex spc dimer' 64: 12 steps. 64: 64: Maximum force: 3.36401e-04 64: 64: 64: Writing Hessian... 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Reading double precision matrix generated by GROMACS 2022.5-Debian_2022.5_2 64: 64: Diagonalizing to find vectors 7 through 18... 64: Writing eigenvalues... 64: 64: Writing average structure & eigenvectors 7--18 to eigenvec.trr 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: There are: 6 Atoms 64: Using begin = 7 and end = 18 64: Full matrix storage format, nrow=18, ncols=18 64: Writing eigenfrequencies - negative eigenvalues will be set to zero. 64: Cannot compute entropy when -first = 7 64: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (1283 ms) 64: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 6.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Small system size (N=3), using full Hessian format. 64: Allocating Hessian memory... 64: 64: starting normal mode calculation '1 TIP5P' 64: 6 steps. 64: 64: Maximum force: 2.42882e-04 64: 64: 64: Writing Hessian... 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Reading double precision matrix generated by GROMACS 2022.5-Debian_2022.5_2 64: 64: Diagonalizing to find vectors 7 through 9... 64: Writing eigenvalues... 64: 64: Writing average structure & eigenvectors 7--9 to eigenvec.trr 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: This run will generate roughly 0 Mb of data 64: There are: 3 Atoms 64: There are: 2 VSites 64: Using begin = 7 and end = 9 64: Full matrix storage format, nrow=9, ncols=9 64: Writing eigenfrequencies - negative eigenvalues will be set to zero. 64: Cannot compute entropy when -first = 7 64: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (919 ms) 64: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: Number of degrees of freedom in T-Coupling group System is 15.00 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Small system size (N=6), using full Hessian format. 64: Allocating Hessian memory... 64: 64: starting normal mode calculation 'sw dimer' 64: 12 steps. 64: 64: Maximum force: 1.07599e-03 64: The force is probably not small enough to ensure that you are at a minimum. 64: Be aware that negative eigenvalues may occur 64: when the resulting matrix is diagonalized. 64: 64: 64: Writing Hessian... 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Reading double precision matrix generated by GROMACS 2022.5-Debian_2022.5_2 64: 64: Diagonalizing to find vectors 7 through 18... 64: Writing eigenvalues... 64: 64: Writing average structure & eigenvectors 7--18 to eigenvec.trr 64: Generated 6 of the 10 non-bonded parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SW' 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: This run will generate roughly 0 Mb of data 64: There are: 6 Atoms 64: There are: 2 Shells 64: There are: 2 VSites 64: 64: NOTE: in the current version shell prediction during the crun is disabled 64: 64: Using begin = 7 and end = 18 64: Full matrix storage format, nrow=18, ncols=18 64: Writing eigenfrequencies - negative eigenvalues will be set to zero. 64: Cannot compute entropy when -first = 7 64: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (22 ms) 64: [----------] 5 tests from NormalModesWorks/NormalModesTest (7392 ms total) 64: 64: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 192.2 64: (ns/day) (hour/ns) 64: Performance: 718.604 0.033 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 64: 64: trr version: GMX_trn_file (double precision) 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 21 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 194.2 64: (ns/day) (hour/ns) 64: Performance: 1910.854 0.013 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (65 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.003 196.7 64: (ns/day) (hour/ns) 64: Performance: 585.107 0.041 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 23 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 194.9 64: (ns/day) (hour/ns) 64: Performance: 2008.671 0.012 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (69 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.036 0.018 199.1 64: (ns/day) (hour/ns) 64: Performance: 80.613 0.298 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 193.9 64: (ns/day) (hour/ns) 64: Performance: 1691.077 0.014 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (58 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.021 0.011 198.6 64: (ns/day) (hour/ns) 64: Performance: 138.736 0.173 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 21 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 194.8 64: (ns/day) (hour/ns) 64: Performance: 1806.626 0.013 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (38 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: NVE simulation: will use the initial temperature of 398.997 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.018 0.009 197.6 64: (ns/day) (hour/ns) 64: Performance: 165.234 0.145 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 91 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.020 0.010 199.1 64: (ns/day) (hour/ns) 64: Performance: 148.095 0.162 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (1222 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: NVE simulation: will use the initial temperature of 398.997 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.025 0.013 198.8 64: (ns/day) (hour/ns) 64: Performance: 117.354 0.205 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 193.9 64: (ns/day) (hour/ns) 64: Performance: 1587.373 0.015 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (683 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.734 to 0.826 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.018 0.009 197.9 64: (ns/day) (hour/ns) 64: Performance: 159.275 0.151 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.734 to 0.826 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 194.6 64: (ns/day) (hour/ns) 64: Performance: 1419.492 0.017 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (925 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.006 197.3 64: (ns/day) (hour/ns) 64: Performance: 255.998 0.094 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 21 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 193.9 64: (ns/day) (hour/ns) 64: Performance: 1487.707 0.016 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (719 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: NVE simulation: will use the initial temperature of 456.887 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 6 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 195.6 64: (ns/day) (hour/ns) 64: Performance: 302.687 0.079 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 194.9 64: (ns/day) (hour/ns) 64: Performance: 984.120 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (53 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: NVE simulation: will use the initial temperature of 456.887 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 6 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 195.7 64: (ns/day) (hour/ns) 64: Performance: 290.279 0.083 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.002 196.7 64: (ns/day) (hour/ns) 64: Performance: 639.663 0.038 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (49 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.020 0.010 198.1 64: (ns/day) (hour/ns) 64: Performance: 142.270 0.169 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 17 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 195.3 64: (ns/day) (hour/ns) 64: Performance: 929.200 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (74 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.017 0.008 197.5 64: (ns/day) (hour/ns) 64: Performance: 173.724 0.138 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.003 196.8 64: (ns/day) (hour/ns) 64: Performance: 587.339 0.041 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (66 ms) 64: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (4027 ms total) 64: 64: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.031 0.016 198.0 64: (ns/day) (hour/ns) 64: Performance: 93.861 0.256 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 786.894 0.030 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (108 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.078 0.039 199.2 64: (ns/day) (hour/ns) 64: Performance: 37.335 0.643 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 195.6 64: (ns/day) (hour/ns) 64: Performance: 846.468 0.028 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (119 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.025 0.013 197.8 64: (ns/day) (hour/ns) 64: Performance: 114.842 0.209 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.6 64: (ns/day) (hour/ns) 64: Performance: 724.350 0.033 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (119 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.046 0.023 198.6 64: (ns/day) (hour/ns) 64: Performance: 62.756 0.382 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.5 64: (ns/day) (hour/ns) 64: Performance: 769.689 0.031 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (105 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.016 0.008 196.4 64: (ns/day) (hour/ns) 64: Performance: 176.714 0.136 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 194.5 64: (ns/day) (hour/ns) 64: Performance: 712.867 0.034 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (84 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.016 0.008 196.5 64: (ns/day) (hour/ns) 64: Performance: 182.072 0.132 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.015 0.008 198.2 64: (ns/day) (hour/ns) 64: Performance: 189.913 0.126 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (59 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 194.6 64: (ns/day) (hour/ns) 64: Performance: 301.119 0.080 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.2 64: (ns/day) (hour/ns) 64: Performance: 775.893 0.031 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (47 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.017 0.008 197.0 64: (ns/day) (hour/ns) 64: Performance: 174.580 0.137 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.3 64: (ns/day) (hour/ns) 64: Performance: 749.191 0.032 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (50 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.017 0.009 195.8 64: (ns/day) (hour/ns) 64: Performance: 166.054 0.145 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 679.527 0.035 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (47 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 194.6 64: (ns/day) (hour/ns) 64: Performance: 308.910 0.078 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.5 64: (ns/day) (hour/ns) 64: Performance: 719.275 0.033 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (48 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.016 0.008 196.2 64: (ns/day) (hour/ns) 64: Performance: 181.477 0.132 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 194.6 64: (ns/day) (hour/ns) 64: Performance: 665.650 0.036 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (52 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.012 0.006 197.9 64: (ns/day) (hour/ns) 64: Performance: 242.868 0.099 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 671.601 0.036 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (48 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.021 0.010 198.7 64: (ns/day) (hour/ns) 64: Performance: 141.845 0.169 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 11 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.1 64: (ns/day) (hour/ns) 64: Performance: 653.297 0.037 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (48 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.006 198.0 64: (ns/day) (hour/ns) 64: Performance: 256.970 0.093 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.2 64: (ns/day) (hour/ns) 64: Performance: 731.662 0.033 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (42 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.027 0.014 199.1 64: (ns/day) (hour/ns) 64: Performance: 108.570 0.221 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 696.979 0.034 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (51 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.017 0.009 198.4 64: (ns/day) (hour/ns) 64: Performance: 167.704 0.143 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.016 0.008 198.3 64: (ns/day) (hour/ns) 64: Performance: 179.751 0.134 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (56 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.018 0.009 198.1 64: (ns/day) (hour/ns) 64: Performance: 163.950 0.146 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.020 0.010 198.7 64: (ns/day) (hour/ns) 64: Performance: 146.444 0.164 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (60 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.030 0.015 199.1 64: (ns/day) (hour/ns) 64: Performance: 97.327 0.247 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.4 64: (ns/day) (hour/ns) 64: Performance: 731.141 0.033 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (55 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.028 0.014 199.1 64: (ns/day) (hour/ns) 64: Performance: 106.067 0.226 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 186.3 64: (ns/day) (hour/ns) 64: Performance: 698.876 0.034 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (59 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.019 0.010 198.7 64: (ns/day) (hour/ns) 64: Performance: 152.569 0.157 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 194.2 64: (ns/day) (hour/ns) 64: Performance: 792.563 0.030 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (51 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.018 0.009 198.5 64: (ns/day) (hour/ns) 64: Performance: 162.112 0.148 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.3 64: (ns/day) (hour/ns) 64: Performance: 700.067 0.034 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (48 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.019 0.009 198.7 64: (ns/day) (hour/ns) 64: Performance: 157.190 0.153 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.3 64: (ns/day) (hour/ns) 64: Performance: 737.884 0.033 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (52 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.025 0.013 197.8 64: (ns/day) (hour/ns) 64: Performance: 116.069 0.207 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.1 64: (ns/day) (hour/ns) 64: Performance: 785.489 0.031 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (70 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.025 0.013 198.0 64: (ns/day) (hour/ns) 64: Performance: 116.323 0.206 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.6 64: (ns/day) (hour/ns) 64: Performance: 715.101 0.034 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (76 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.033 0.017 198.2 64: (ns/day) (hour/ns) 64: Performance: 88.297 0.272 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 778.836 0.031 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (77 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.023 0.012 197.5 64: (ns/day) (hour/ns) 64: Performance: 126.699 0.189 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 70 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.013 0.006 198.1 64: (ns/day) (hour/ns) 64: Performance: 231.506 0.104 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (81 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.023 0.012 197.8 64: (ns/day) (hour/ns) 64: Performance: 127.030 0.189 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.020 0.010 198.7 64: (ns/day) (hour/ns) 64: Performance: 144.367 0.166 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (87 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.005 195.3 64: (ns/day) (hour/ns) 64: Performance: 272.834 0.088 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 11 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.003 195.6 64: (ns/day) (hour/ns) 64: Performance: 575.058 0.042 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (81 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.033 0.017 198.4 64: (ns/day) (hour/ns) 64: Performance: 88.698 0.271 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 71 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.012 0.006 198.1 64: (ns/day) (hour/ns) 64: Performance: 243.656 0.098 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (82 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 195.6 64: (ns/day) (hour/ns) 64: Performance: 309.407 0.078 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.002 195.2 64: (ns/day) (hour/ns) 64: Performance: 621.592 0.039 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (67 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.012 0.006 196.1 64: (ns/day) (hour/ns) 64: Performance: 242.257 0.099 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 11 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.002 196.2 64: (ns/day) (hour/ns) 64: Performance: 609.477 0.039 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (72 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.028 0.014 198.3 64: (ns/day) (hour/ns) 64: Performance: 105.781 0.227 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.003 194.8 64: (ns/day) (hour/ns) 64: Performance: 587.003 0.041 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (76 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.024 0.012 197.7 64: (ns/day) (hour/ns) 64: Performance: 119.994 0.200 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.012 0.006 198.0 64: (ns/day) (hour/ns) 64: Performance: 244.032 0.098 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (79 ms) 64: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (2276 ms total) 64: 64: [----------] 2 tests from Angles1/SimpleMdrunTest 64: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file angles1.top, line 72]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group System is 9.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 238.919 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'This_incredible_box_of_butane' 64: 50 steps, 0.1 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.012 0.006 196.8 64: (ns/day) (hour/ns) 64: Performance: 745.053 0.032 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 64: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (32 ms) 64: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file angles1.top, line 72]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group System is 9.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 238.919 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'This_incredible_box_of_butane' 64: 50 steps, 0.1 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.026 0.013 199.1 64: (ns/day) (hour/ns) 64: Performance: 334.131 0.072 64: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 64: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (37 ms) 64: [----------] 2 tests from Angles1/SimpleMdrunTest (70 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 65 tests from 7 test suites ran. (18469 ms total) 64: [ PASSED ] 65 tests. 64/81 Test #64: MdrunNonIntegratorTests ........................ Passed 18.53 sec test 65 Start 65: MdrunTpiTests 65: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 2 tests from 1 test suite. 65: [----------] Global test environment set-up. 65: [----------] 2 tests from Simple/TpiTest 65: [ RUN ] Simple/TpiTest.ReproducesOutput/0 65: Ignoring obsolete mdp entry 'ns_type' 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 1308.00 65: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 65: log). 65: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 65: TPI is not implemented for GPUs. 65: 65: Using 1 MPI thread 65: Using 1 OpenMP thread 65: 65: 65: NOTE: Thread affinity was not set. 65: Reading frames from gro file '216 water molecules', 648 atoms. 65: Reading frame 0 time 0.000 mu 3.905e+02 3.905e+02 65: Last frame 0 time 0.000 65: Generated 331705 of the 331705 non-bonded parameter combinations 65: 65: Generated 331705 of the 331705 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Excluding 3 bonded neighbours molecule type 'methane' 65: Analysing residue names: 65: There are: 216 Water residues 65: There are: 1 Other residues 65: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] Simple/TpiTest.ReproducesOutput/0 (752 ms) 65: [ RUN ] Simple/TpiTest.ReproducesOutput/1 65: Ignoring obsolete mdp entry 'ns_type' 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 1308.00 65: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 65: log). 65: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 65: TPI is not implemented for GPUs. 65: 65: Using 1 MPI thread 65: Using 1 OpenMP thread 65: 65: 65: NOTE: Thread affinity was not set. 65: Reading frames from gro file '216 water molecules', 648 atoms. 65: Reading frame 0 time 0.000 mu 1.070e+02 1.070e+02 65: Last frame 0 time 0.000 65: Generated 331705 of the 331705 non-bonded parameter combinations 65: 65: Generated 331705 of the 331705 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Excluding 3 bonded neighbours molecule type 'methane' 65: Analysing residue names: 65: There are: 216 Water residues 65: There are: 1 Other residues 65: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] Simple/TpiTest.ReproducesOutput/1 (600 ms) 65: [----------] 2 tests from Simple/TpiTest (1353 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 2 tests from 1 test suite ran. (1503 ms total) 65: [ PASSED ] 2 tests. 65/81 Test #65: MdrunTpiTests .................................. Passed 1.55 sec test 66 Start 66: MdrunMpiTests 66: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 17 tests from 4 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from DomainDecompositionSpecialCasesTest 66: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 0 steps, 0.0 ps. 66: 66: NOTE: 55 % of the run time was spent in domain decomposition, 66: 0 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: NOTE: 24 % of the run time was spent communicating energies, 66: you might want to increase some nst* mdp options 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.160 0.040 398.2 66: (ns/day) (hour/ns) 66: Performance: 2.151 11.158 66: Setting the LD random seed to -5984323 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (212 ms) 66: [----------] 1 test from DomainDecompositionSpecialCasesTest (212 ms total) 66: 66: [----------] 4 tests from MimicTest 66: [ RUN ] MimicTest.OneQuantumMol 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 21.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 66: 66: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 98 % of the run time was spent in domain decomposition, 66: 0 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.146 0.036 399.5 66: (ns/day) (hour/ns) 66: Performance: 2.368 10.136 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -872450305 66: 66: Generated 10 of the 10 non-bonded parameter combinations 66: 66: Generated 10 of the 10 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MimicTest.OneQuantumMol (268 ms) 66: [ RUN ] MimicTest.AllQuantumMol 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 21.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 66: 66: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 79 % of the run time was spent in domain decomposition, 66: 0 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.121 0.030 399.5 66: (ns/day) (hour/ns) 66: Performance: 2.844 8.438 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -36765734 66: 66: Generated 10 of the 10 non-bonded parameter combinations 66: 66: Generated 10 of the 10 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MimicTest.AllQuantumMol (152 ms) 66: [ RUN ] MimicTest.TwoQuantumMol 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 21.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 66: 66: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 20 % of the run time was spent in domain decomposition, 66: 11 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: NOTE: 6 % of the run time was spent communicating energies, 66: you might want to increase some nst* mdp options 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.002 0.001 375.8 66: (ns/day) (hour/ns) 66: Performance: 138.501 0.173 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -570971283 66: 66: Generated 10 of the 10 non-bonded parameter combinations 66: 66: Generated 10 of the 10 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MimicTest.TwoQuantumMol (107 ms) 66: [ RUN ] MimicTest.BondCuts 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 66.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 66: NVE simulation: will use the initial temperature of 300.368 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/ala.gro' 66: 66: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.025 0.006 397.5 66: (ns/day) (hour/ns) 66: Performance: 13.499 1.778 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1006411775 66: 66: Generated 2211 of the 2211 non-bonded parameter combinations 66: 66: Generated 2211 of the 2211 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MimicTest.BondCuts (227 ms) 66: [----------] 4 tests from MimicTest (755 ms total) 66: 66: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -4.79910463671057e+01 66: Maximum force = 1.86297359432216e+02 on atom 13 66: Norm of force = 8.77219865482119e+01 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 66: 66: Generated 330891 of the 330891 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2568 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 3.02331e+02 on atom 3 66: F-Norm = 1.18024e+02 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -5.58622538633291e+01 66: Maximum force = 4.27274822366504e+02 on atom 13 66: Norm of force = 1.84530029253830e+02 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 66: 66: Generated 330891 of the 330891 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (781 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 1 66: Number of degrees of freedom in T-Coupling group System is 22.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 3.19376899751522e+02 66: Maximum force = 9.99884921009767e+03 on atom 9 66: Norm of force = 4.61669565054298e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: turning H bonds into constraints... 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (515 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 1 66: 66: NOTE 3 [file glycine_vacuo.top, line 12]: 66: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 66: 66: Number of degrees of freedom in T-Coupling group System is 22.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 2.41575e+04 on atom 10 66: F-Norm = 1.18451e+04 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 1.51743018140927e+02 66: Maximum force = 7.42089573409110e+03 on atom 9 66: Norm of force = 3.56929298615739e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: turning H bonds into constraints... 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (189 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -1.56984193848274e+02 66: Maximum force = 4.56923624626478e+02 on atom 17 66: Norm of force = 1.83258377168370e+02 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (158 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: 66: NOTE 4 [file unknown]: 66: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 66: 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 1.06800e+03 on atom 28 66: F-Norm = 4.26922e+02 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -1.69410778678186e+02 66: Maximum force = 2.18225948474111e+02 on atom 17 66: Norm of force = 7.92068036537837e+01 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (354 ms) 66: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (4568 ms total) 66: 66: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents converged to Fmax < 10 in 1 steps 66: Potential Energy = -9.74257075835447e-01 66: Maximum force = 4.01322929015133e+00 on atom 3 66: Norm of force = 1.63839399694378e+00 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (149 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 4.01323e+00 on atom 3 66: F-Norm = 1.63839e+00 66: 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 66: Potential Energy = -9.90642313893969e-01 66: Maximum force = 2.57812909490791e+00 on atom 3 66: Norm of force = 1.05251679559130e+00 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (148 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 66: 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 notes 66: 66: There was 1 warning 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (5 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 1 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 3.19395484891519e+02 66: Maximum force = 9.97041707197910e+03 on atom 9 66: Norm of force = 4.62274878665467e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (413 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 1 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 66: Using 2 MPI threads 66: Using 2 OpenMP threads per tMPI thread 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 2.41672e+04 on atom 10 66: F-Norm = 1.19357e+04 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 1.56258793899480e+02 66: Maximum force = 7.50181017480397e+03 on atom 9 66: Norm of force = 3.61390332564874e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (320 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 66: 66: Generating 1-4 interactions: fudge = 1 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: 66: There was 1 warning 66: Generated 20503 of the 20503 non-bonded parameter combinations 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (152 ms) 66: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1188 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 17 tests from 4 test suites ran. (7315 ms total) 66: [ PASSED ] 17 tests. 66/81 Test #66: MdrunMpiTests .................................. Passed 7.38 sec test 67 Start 67: MdrunMultiSimTests 67: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMultiSimTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 2 tests from 1 test suite. 67: [----------] Global test environment set-up. 67: [----------] 2 tests from InNvt/MultiSimTerminationTest 67: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 67: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 67: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 67: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 67: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 2 tests from 1 test suite ran. (155 ms total) 67: [ PASSED ] 2 tests. 67: 67: YOU HAVE 4 DISABLED TESTS 67: 67/81 Test #67: MdrunMultiSimTests ............................. Passed 0.21 sec test 68 Start 68: MdrunMultiSimReplexTests 68: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 1 test from 1 test suite. 68: [----------] Global test environment set-up. 68: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 68: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 68: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 68: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 1 test from 1 test suite ran. (159 ms total) 68: [ PASSED ] 1 test. 68: 68: YOU HAVE 4 DISABLED TESTS 68: 68/81 Test #68: MdrunMultiSimReplexTests ....................... Passed 0.21 sec test 69 Start 69: MdrunMultiSimReplexEquivalenceTests 69: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 0 tests from 0 test suites. 69: [==========] 0 tests from 0 test suites ran. (0 ms total) 69: [ PASSED ] 0 tests. 69: 69: YOU HAVE 10 DISABLED TESTS 69: 69/81 Test #69: MdrunMultiSimReplexEquivalenceTests ............ Passed 0.05 sec test 70 Start 70: MdrunMpi1RankPmeTests 70: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 19 tests from 1 test suite. 70: [----------] Global test environment set-up. 70: [----------] 19 tests from ReproducesEnergies/PmeTest 70: Number of degrees of freedom in T-Coupling group rest is 12.00 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: NVE simulation: will use the initial temperature of 1046.791 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 2 notes 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: Number of degrees of freedom in T-Coupling group rest is 13.00 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: NVE simulation: will use the initial temperature of 966.268 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 notes 70: Setting the LD random seed to -12583186 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: The largest distance between excluded atoms is 0.190 nm 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 70: 70: Estimate for the relative computational load of the PME mesh part: 1.00 70: 70: This run will generate roughly 0 Mb of data 70: Setting the LD random seed to -270553153 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Searching the wall atom type(s) 70: 70: The largest distance between excluded atoms is 0.190 nm 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 70: 70: Estimate for the relative computational load of the PME mesh part: 1.00 70: 70: This run will generate roughly 0 Mb of data 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 70: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc-and-methanol' 70: 20 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: NOTE: 31 % of the run time was spent in domain decomposition, 70: 0 % of the run time was spent in pair search, 70: you might want to increase nstlist (this has no effect on accuracy) 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.258 0.129 199.8 70: (ns/day) (hour/ns) 70: Performance: 14.078 1.705 70: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (579 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 70: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc-and-methanol' 70: 20 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.142 0.071 199.6 70: (ns/day) (hour/ns) 70: Performance: 25.556 0.939 70: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (98 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 70: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc-and-methanol' 70: 0 steps, 0.0 ps. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.024 0.012 197.9 70: (ns/day) (hour/ns) 70: Performance: 7.016 3.421 70: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (1427 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 70: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI thread 70: Using 2 OpenMP threads 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: starting mdrun 'spc-and-methanol' 70: 20 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.221 0.111 199.8 70: (ns/day) (hour/ns) 70: Performance: 16.389 1.464 70: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as double precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (173 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Double-precision build of GROMACS. 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 70: [----------] 19 tests from ReproducesEnergies/PmeTest (2281 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 19 tests from 1 test suite ran. (2467 ms total) 70: [ PASSED ] 4 tests. 70: [ SKIPPED ] 15 tests, listed below: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 70/81 Test #70: MdrunMpi1RankPmeTests .......................... Passed 2.53 sec test 71 Start 71: MdrunMpi2RankPmeTests 71: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 19 tests from 1 test suite. 71: [----------] Global test environment set-up. 71: [----------] 19 tests from ReproducesEnergies/PmeTest 71: Number of degrees of freedom in T-Coupling group rest is 12.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: NVE simulation: will use the initial temperature of 1046.791 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 notes 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Number of degrees of freedom in T-Coupling group rest is 13.00 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: NVE simulation: will use the initial temperature of 966.268 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 3 notes 71: Setting the LD random seed to -372995 71: 71: Generated 8 of the 10 non-bonded parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'Methanol' 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: The largest distance between excluded atoms is 0.190 nm 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to 2125954941 71: 71: Generated 8 of the 10 non-bonded parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'Methanol' 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Searching the wall atom type(s) 71: 71: The largest distance between excluded atoms is 0.190 nm 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was off during the run due to low measured imbalance. 71: Average load imbalance: 0.7%. 71: The balanceable part of the MD step is 8%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 0.1%. 71: 71: 71: NOTE: 13 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 2.270 0.568 399.9 71: (ns/day) (hour/ns) 71: Performance: 3.196 7.510 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (1082 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was off during the run due to low measured imbalance. 71: Average load imbalance: 7.9%. 71: The balanceable part of the MD step is 6%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 0.4%. 71: 71: 71: Core t (s) Wall t (s) (%) 71: Time: 2.256 0.564 399.9 71: (ns/day) (hour/ns) 71: Performance: 3.216 7.463 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (815 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 0 steps, 0.0 ps. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.013 0.003 379.8 71: (ns/day) (hour/ns) 71: Performance: 24.922 0.963 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (1251 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 1.069 0.267 399.8 71: (ns/day) (hour/ns) 71: Performance: 6.784 3.538 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_cpu.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (507 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.714 0.179 399.8 71: (ns/day) (hour/ns) 71: Performance: 10.154 2.364 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_auto.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (300 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 0 steps, 0.0 ps. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.064 0.016 396.4 71: (ns/day) (hour/ns) 71: Performance: 5.370 4.470 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_1_pme_cpu.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (1122 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was turned on during the run due to measured imbalance. 71: Average load imbalance: 24.2%. 71: The balanceable part of the MD step is 12%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 2.9%. 71: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 71: 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.436 0.109 399.6 71: (ns/day) (hour/ns) 71: Performance: 16.623 1.444 71: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (329 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 71: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 71: Test is being skipped because: 71: it targets GPU execution, but no compatible devices were detected 71: it targets PME decomposition, but that is not supported 71: PME GPU does not support: 71: Double-precision build of GROMACS. 71: Non-GPU build of GROMACS. 71: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 71: [----------] 19 tests from ReproducesEnergies/PmeTest (5411 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 19 tests from 1 test suite ran. (5581 ms total) 71: [ PASSED ] 7 tests. 71: [ SKIPPED ] 12 tests, listed below: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 71/81 Test #71: MdrunMpi2RankPmeTests .......................... Passed 5.62 sec test 72 Start 72: MdrunMpiCoordinationBasicTestsOneRank 72: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-mpi-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationBasicTestsOneRank.xml" 72: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 72: Test timeout computed to be: 1920 72: [==========] Running 1 test from 1 test suite. 72: [----------] Global test environment set-up. 72: [----------] 1 test from BasicPropagators/PeriodicActionsTest 72: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (1) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.008 0.009 99.1 72: (ns/day) (hour/ns) 72: Performance: 172.021 0.140 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (1) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 96.1 72: (ns/day) (hour/ns) 72: Performance: 846.701 0.028 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 5 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 95.1 72: (ns/day) (hour/ns) 72: Performance: 847.749 0.028 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 4 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.010 0.010 98.7 72: (ns/day) (hour/ns) 72: Performance: 140.557 0.171 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 4 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 96.0 72: (ns/day) (hour/ns) 72: Performance: 786.291 0.031 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 4 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI thread 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 95.8 72: (ns/day) (hour/ns) 72: Performance: 707.301 0.034 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 72: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (150 ms) 72: [----------] 1 test from BasicPropagators/PeriodicActionsTest (150 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 1 test from 1 test suite ran. (322 ms total) 72: [ PASSED ] 1 test. 72/81 Test #72: MdrunMpiCoordinationBasicTestsOneRank .......... Passed 0.37 sec test 73 Start 73: MdrunMpiCoordinationBasicTestsTwoRanks 73: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-mpi-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationBasicTestsTwoRanks.xml" 73: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 73: Test timeout computed to be: 1920 73: [==========] Running 1 test from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 1 test from BasicPropagators/PeriodicActionsTest 73: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: Setting nstcalcenergy (100) equal to nstenergy (1) 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: There were 3 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 0.2%. 73: The balanceable part of the MD step is 64%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 0.2%. 73: 73: 73: NOTE: 41 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.018 0.009 197.6 73: (ns/day) (hour/ns) 73: Performance: 160.484 0.150 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: Setting nstcalcenergy (100) equal to nstenergy (1) 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: There were 3 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 0.8%. 73: The balanceable part of the MD step is 61%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 0.5%. 73: 73: 73: NOTE: 26 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.005 0.002 192.0 73: (ns/day) (hour/ns) 73: Performance: 595.140 0.040 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: Setting nstcalcenergy (100) equal to nstenergy (4) 73: 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 5 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 2.7%. 73: The balanceable part of the MD step is 59%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 1.6%. 73: 73: 73: NOTE: 27 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.004 0.002 192.3 73: (ns/day) (hour/ns) 73: Performance: 630.756 0.038 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 4 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 1.2%. 73: The balanceable part of the MD step is 58%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 0.7%. 73: 73: 73: NOTE: 29 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.005 0.002 192.1 73: (ns/day) (hour/ns) 73: Performance: 620.308 0.039 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 4 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 1.8%. 73: The balanceable part of the MD step is 58%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 1.1%. 73: 73: 73: NOTE: 30 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.004 0.002 190.6 73: (ns/day) (hour/ns) 73: Performance: 635.244 0.038 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 4 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI threads 73: Using 1 OpenMP thread per tMPI thread 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 1.3%. 73: The balanceable part of the MD step is 56%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 0.7%. 73: 73: 73: NOTE: 31 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.005 0.002 191.6 73: (ns/day) (hour/ns) 73: Performance: 608.484 0.039 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 73: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (385 ms) 73: [----------] 1 test from BasicPropagators/PeriodicActionsTest (385 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (564 ms total) 73: [ PASSED ] 1 test. 73/81 Test #73: MdrunMpiCoordinationBasicTestsTwoRanks ......... Passed 0.62 sec test 74 Start 74: MdrunMpiCoordinationCouplingTestsOneRank 74: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-mpi-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationCouplingTestsOneRank.xml" 74: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 74: Test timeout computed to be: 1920 74: [==========] Running 22 tests from 1 test suite. 74: [----------] Global test environment set-up. 74: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.005 98.3 74: (ns/day) (hour/ns) 74: Performance: 314.268 0.076 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.8 74: (ns/day) (hour/ns) 74: Performance: 744.753 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.1 74: (ns/day) (hour/ns) 74: Performance: 914.849 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.006 98.5 74: (ns/day) (hour/ns) 74: Performance: 250.890 0.096 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.6 74: (ns/day) (hour/ns) 74: Performance: 791.240 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 725.117 0.033 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (134 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.1 74: (ns/day) (hour/ns) 74: Performance: 546.491 0.044 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 799.973 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.3 74: (ns/day) (hour/ns) 74: Performance: 767.771 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 96.8 74: (ns/day) (hour/ns) 74: Performance: 494.986 0.048 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.5 74: (ns/day) (hour/ns) 74: Performance: 853.741 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 92.8 74: (ns/day) (hour/ns) 74: Performance: 651.846 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (63 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.3 74: (ns/day) (hour/ns) 74: Performance: 625.251 0.038 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.003 96.6 74: (ns/day) (hour/ns) 74: Performance: 567.692 0.042 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 773.070 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.6 74: (ns/day) (hour/ns) 74: Performance: 902.916 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 700.625 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.3 74: (ns/day) (hour/ns) 74: Performance: 831.614 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (62 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.4 74: (ns/day) (hour/ns) 74: Performance: 541.258 0.044 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 870.878 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.5 74: (ns/day) (hour/ns) 74: Performance: 834.430 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 907.705 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.4 74: (ns/day) (hour/ns) 74: Performance: 710.892 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 839.089 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (60 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.3 74: (ns/day) (hour/ns) 74: Performance: 519.180 0.046 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 846.003 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.0 74: (ns/day) (hour/ns) 74: Performance: 926.963 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 700.067 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 855.638 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.4 74: (ns/day) (hour/ns) 74: Performance: 763.868 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (62 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.003 86.9 74: (ns/day) (hour/ns) 74: Performance: 552.371 0.043 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.7 74: (ns/day) (hour/ns) 74: Performance: 662.145 0.036 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 825.928 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 875.582 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 871.988 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 895.956 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (60 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.6 74: (ns/day) (hour/ns) 74: Performance: 606.477 0.040 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 795.326 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.6 74: (ns/day) (hour/ns) 74: Performance: 901.858 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 753.958 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 855.044 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 788.506 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (58 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.9 74: (ns/day) (hour/ns) 74: Performance: 692.746 0.035 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 89.6 74: (ns/day) (hour/ns) 74: Performance: 876.080 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.002 95.2 74: (ns/day) (hour/ns) 74: Performance: 963.798 0.025 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 93.1 74: (ns/day) (hour/ns) 74: Performance: 831.838 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 769.305 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 804.150 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (57 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 96.7 74: (ns/day) (hour/ns) 74: Performance: 565.451 0.042 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.6 74: (ns/day) (hour/ns) 74: Performance: 723.074 0.033 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 915.121 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 777.460 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 878.829 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 774.430 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (57 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.7 74: (ns/day) (hour/ns) 74: Performance: 626.140 0.038 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 860.899 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.1 74: (ns/day) (hour/ns) 74: Performance: 896.347 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 81.9 74: (ns/day) (hour/ns) 74: Performance: 696.034 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 762.733 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.6 74: (ns/day) (hour/ns) 74: Performance: 840.463 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (58 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.4 74: (ns/day) (hour/ns) 74: Performance: 538.043 0.045 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 772.488 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 802.370 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 868.546 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 850.323 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 799.454 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (57 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.6 74: (ns/day) (hour/ns) 74: Performance: 672.040 0.036 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.6 74: (ns/day) (hour/ns) 74: Performance: 916.073 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 96.4 74: (ns/day) (hour/ns) 74: Performance: 1034.698 0.023 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 1037.836 0.023 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.7 74: (ns/day) (hour/ns) 74: Performance: 941.555 0.025 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.5 74: (ns/day) (hour/ns) 74: Performance: 829.374 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (56 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.2 74: (ns/day) (hour/ns) 74: Performance: 654.408 0.037 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.6 74: (ns/day) (hour/ns) 74: Performance: 772.682 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.4 74: (ns/day) (hour/ns) 74: Performance: 645.494 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.8 74: (ns/day) (hour/ns) 74: Performance: 793.993 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.9 74: (ns/day) (hour/ns) 74: Performance: 781.107 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.8 74: (ns/day) (hour/ns) 74: Performance: 697.057 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (60 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.0 74: (ns/day) (hour/ns) 74: Performance: 668.177 0.036 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.8 74: (ns/day) (hour/ns) 74: Performance: 705.438 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 870.878 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.5 74: (ns/day) (hour/ns) 74: Performance: 838.062 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.4 74: (ns/day) (hour/ns) 74: Performance: 890.774 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 839.204 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (61 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.6 74: (ns/day) (hour/ns) 74: Performance: 556.613 0.043 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.3 74: (ns/day) (hour/ns) 74: Performance: 660.512 0.036 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.9 74: (ns/day) (hour/ns) 74: Performance: 714.272 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.5 74: (ns/day) (hour/ns) 74: Performance: 647.121 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.9 74: (ns/day) (hour/ns) 74: Performance: 671.381 0.036 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.4 74: (ns/day) (hour/ns) 74: Performance: 670.504 0.036 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (71 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.7 74: (ns/day) (hour/ns) 74: Performance: 383.455 0.063 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.2 74: (ns/day) (hour/ns) 74: Performance: 615.505 0.039 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.2 74: (ns/day) (hour/ns) 74: Performance: 651.226 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.3 74: (ns/day) (hour/ns) 74: Performance: 374.390 0.064 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.2 74: (ns/day) (hour/ns) 74: Performance: 644.279 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.3 74: (ns/day) (hour/ns) 74: Performance: 611.231 0.039 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (77 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 97.9 74: (ns/day) (hour/ns) 74: Performance: 377.487 0.064 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.9 74: (ns/day) (hour/ns) 74: Performance: 660.158 0.036 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.003 97.2 74: (ns/day) (hour/ns) 74: Performance: 576.943 0.042 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 97.9 74: (ns/day) (hour/ns) 74: Performance: 406.184 0.059 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.0 74: (ns/day) (hour/ns) 74: Performance: 456.002 0.053 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.9 74: (ns/day) (hour/ns) 74: Performance: 504.140 0.048 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (73 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.1 74: (ns/day) (hour/ns) 74: Performance: 381.697 0.063 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 97.9 74: (ns/day) (hour/ns) 74: Performance: 389.467 0.062 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.3 74: (ns/day) (hour/ns) 74: Performance: 712.290 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.0 74: (ns/day) (hour/ns) 74: Performance: 460.261 0.052 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.7 74: (ns/day) (hour/ns) 74: Performance: 458.855 0.052 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.8 74: (ns/day) (hour/ns) 74: Performance: 466.676 0.051 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (75 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.9 74: (ns/day) (hour/ns) 74: Performance: 422.363 0.057 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.003 72.2 74: (ns/day) (hour/ns) 74: Performance: 501.350 0.048 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.8 74: (ns/day) (hour/ns) 74: Performance: 462.542 0.052 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.6 74: (ns/day) (hour/ns) 74: Performance: 519.794 0.046 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.6 74: (ns/day) (hour/ns) 74: Performance: 473.600 0.051 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.5 74: (ns/day) (hour/ns) 74: Performance: 461.779 0.052 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (72 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.3 74: (ns/day) (hour/ns) 74: Performance: 373.030 0.064 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 95.1 74: (ns/day) (hour/ns) 74: Performance: 438.914 0.055 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.0 74: (ns/day) (hour/ns) 74: Performance: 610.746 0.039 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.1 74: (ns/day) (hour/ns) 74: Performance: 402.890 0.060 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.6 74: (ns/day) (hour/ns) 74: Performance: 478.418 0.050 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.8 74: (ns/day) (hour/ns) 74: Performance: 440.767 0.054 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (75 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.005 98.1 74: (ns/day) (hour/ns) 74: Performance: 316.887 0.076 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.7 74: (ns/day) (hour/ns) 74: Performance: 420.461 0.057 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.005 98.4 74: (ns/day) (hour/ns) 74: Performance: 311.550 0.077 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.004 97.6 74: (ns/day) (hour/ns) 74: Performance: 418.917 0.057 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.005 98.1 74: (ns/day) (hour/ns) 74: Performance: 305.025 0.079 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.8 74: (ns/day) (hour/ns) 74: Performance: 434.947 0.055 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (81 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.4 74: (ns/day) (hour/ns) 74: Performance: 377.835 0.064 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.6 74: (ns/day) (hour/ns) 74: Performance: 459.471 0.052 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.9 74: (ns/day) (hour/ns) 74: Performance: 442.444 0.054 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.0 74: (ns/day) (hour/ns) 74: Performance: 451.028 0.053 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 97.9 74: (ns/day) (hour/ns) 74: Performance: 379.791 0.063 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI thread 74: Using 1 OpenMP thread 74: 74: 74: NOTE: Thread affinity was not set. 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.5 74: (ns/day) (hour/ns) 74: Performance: 395.696 0.061 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (77 ms) 74: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (1517 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 22 tests from 1 test suite ran. (1694 ms total) 74: [ PASSED ] 22 tests. 74/81 Test #74: MdrunMpiCoordinationCouplingTestsOneRank ....... Passed 1.75 sec test 75 Start 75: MdrunMpiCoordinationCouplingTestsTwoRanks 75: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-mpi-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationCouplingTestsTwoRanks.xml" 75: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 75: Test timeout computed to be: 1920 75: [==========] Running 22 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.4%. 75: The balanceable part of the MD step is 61%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.2%. 75: 75: 75: NOTE: 39 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.013 0.006 197.0 75: (ns/day) (hour/ns) 75: Performance: 227.265 0.106 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.5%. 75: The balanceable part of the MD step is 59%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.9%. 75: 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.6 75: (ns/day) (hour/ns) 75: Performance: 678.779 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 7.3%. 75: The balanceable part of the MD step is 51%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 3.7%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 186.3 75: (ns/day) (hour/ns) 75: Performance: 715.849 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 5.9%. 75: The balanceable part of the MD step is 49%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.9%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 636.820 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 3.9%. 75: The balanceable part of the MD step is 49%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.9%. 75: 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.5 75: (ns/day) (hour/ns) 75: Performance: 657.235 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.2%. 75: The balanceable part of the MD step is 51%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.1%. 75: 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.3 75: (ns/day) (hour/ns) 75: Performance: 720.832 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (348 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.0%. 75: The balanceable part of the MD step is 63%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.6%. 75: 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.005 194.9 75: (ns/day) (hour/ns) 75: Performance: 313.836 0.076 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 3.6%. 75: The balanceable part of the MD step is 58%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.1%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.8 75: (ns/day) (hour/ns) 75: Performance: 743.853 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.0%. 75: The balanceable part of the MD step is 57%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.1%. 75: 75: 75: NOTE: 89 % of the run time was spent in domain decomposition, 75: 0 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.068 0.034 199.5 75: (ns/day) (hour/ns) 75: Performance: 42.956 0.559 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 6.0%. 75: The balanceable part of the MD step is 54%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 3.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.9 75: (ns/day) (hour/ns) 75: Performance: 741.793 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 5.2%. 75: The balanceable part of the MD step is 53%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.7%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.5 75: (ns/day) (hour/ns) 75: Performance: 776.431 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.0%. 75: The balanceable part of the MD step is 52%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.0%. 75: 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.9 75: (ns/day) (hour/ns) 75: Performance: 802.683 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (415 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 3.7%. 75: The balanceable part of the MD step is 60%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 193.5 75: (ns/day) (hour/ns) 75: Performance: 588.095 0.041 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 4.9%. 75: The balanceable part of the MD step is 57%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.8%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 25 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 193.1 75: (ns/day) (hour/ns) 75: Performance: 686.188 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 5.4%. 75: The balanceable part of the MD step is 54%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.9%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.6 75: (ns/day) (hour/ns) 75: Performance: 784.289 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 4.2%. 75: The balanceable part of the MD step is 54%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.3%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.8 75: (ns/day) (hour/ns) 75: Performance: 753.313 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 9.0%. 75: The balanceable part of the MD step is 52%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 4.7%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.4 75: (ns/day) (hour/ns) 75: Performance: 709.787 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 4.2%. 75: The balanceable part of the MD step is 54%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.3%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.8 75: (ns/day) (hour/ns) 75: Performance: 783.940 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (350 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 47 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 1.913 0.972 196.8 75: (ns/day) (hour/ns) 75: Performance: 1.511 15.882 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 190.6 75: (ns/day) (hour/ns) 75: Performance: 810.658 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 189.6 75: (ns/day) (hour/ns) 75: Performance: 820.428 0.029 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.9 75: (ns/day) (hour/ns) 75: Performance: 693.487 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.3 75: (ns/day) (hour/ns) 75: Performance: 641.829 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 35 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.6 75: (ns/day) (hour/ns) 75: Performance: 622.062 0.039 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (2034 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 16 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.031 19.0 75: (ns/day) (hour/ns) 75: Performance: 47.450 0.506 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.9 75: (ns/day) (hour/ns) 75: Performance: 629.338 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 190.2 75: (ns/day) (hour/ns) 75: Performance: 606.417 0.040 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 44 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.013 0.007 196.3 75: (ns/day) (hour/ns) 75: Performance: 222.236 0.108 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.1 75: (ns/day) (hour/ns) 75: Performance: 701.742 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.3 75: (ns/day) (hour/ns) 75: Performance: 697.413 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (365 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 191.7 75: (ns/day) (hour/ns) 75: Performance: 520.782 0.046 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 187.9 75: (ns/day) (hour/ns) 75: Performance: 646.646 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.3 75: (ns/day) (hour/ns) 75: Performance: 662.251 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.5 75: (ns/day) (hour/ns) 75: Performance: 705.237 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.9 75: (ns/day) (hour/ns) 75: Performance: 700.824 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.4 75: (ns/day) (hour/ns) 75: Performance: 627.192 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (349 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 24 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 192.9 75: (ns/day) (hour/ns) 75: Performance: 449.760 0.053 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.6 75: (ns/day) (hour/ns) 75: Performance: 660.299 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 35 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 192.2 75: (ns/day) (hour/ns) 75: Performance: 505.983 0.047 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.2 75: (ns/day) (hour/ns) 75: Performance: 639.232 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.0 75: (ns/day) (hour/ns) 75: Performance: 647.393 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 190.7 75: (ns/day) (hour/ns) 75: Performance: 834.769 0.029 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (312 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 22 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.021 26.7 75: (ns/day) (hour/ns) 75: Performance: 69.395 0.346 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.2 75: (ns/day) (hour/ns) 75: Performance: 701.622 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 190.4 75: (ns/day) (hour/ns) 75: Performance: 906.570 0.026 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.5 75: (ns/day) (hour/ns) 75: Performance: 726.614 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.3 75: (ns/day) (hour/ns) 75: Performance: 691.192 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 183.4 75: (ns/day) (hour/ns) 75: Performance: 768.921 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (367 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 191.6 75: (ns/day) (hour/ns) 75: Performance: 516.438 0.046 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.7 75: (ns/day) (hour/ns) 75: Performance: 649.920 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.8 75: (ns/day) (hour/ns) 75: Performance: 664.717 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.5 75: (ns/day) (hour/ns) 75: Performance: 633.969 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.8 75: (ns/day) (hour/ns) 75: Performance: 643.639 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.0 75: (ns/day) (hour/ns) 75: Performance: 639.563 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (340 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 25 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.6 75: (ns/day) (hour/ns) 75: Performance: 485.985 0.049 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.5 75: (ns/day) (hour/ns) 75: Performance: 761.507 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.5 75: (ns/day) (hour/ns) 75: Performance: 743.001 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 47 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.074 0.045 164.7 75: (ns/day) (hour/ns) 75: Performance: 32.669 0.735 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.7 75: (ns/day) (hour/ns) 75: Performance: 713.032 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.6 75: (ns/day) (hour/ns) 75: Performance: 687.298 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (451 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 24 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 193.0 75: (ns/day) (hour/ns) 75: Performance: 657.937 0.036 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.6 75: (ns/day) (hour/ns) 75: Performance: 663.571 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.028 0.014 198.4 75: (ns/day) (hour/ns) 75: Performance: 102.455 0.234 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.0 75: (ns/day) (hour/ns) 75: Performance: 737.663 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.7 75: (ns/day) (hour/ns) 75: Performance: 660.937 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.0 75: (ns/day) (hour/ns) 75: Performance: 720.664 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (376 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 193.2 75: (ns/day) (hour/ns) 75: Performance: 537.456 0.045 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.5 75: (ns/day) (hour/ns) 75: Performance: 744.258 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 191.6 75: (ns/day) (hour/ns) 75: Performance: 821.194 0.029 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.5 75: (ns/day) (hour/ns) 75: Performance: 754.328 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.7 75: (ns/day) (hour/ns) 75: Performance: 701.143 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.2 75: (ns/day) (hour/ns) 75: Performance: 770.652 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (298 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 19 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.005 152.6 75: (ns/day) (hour/ns) 75: Performance: 294.371 0.082 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.0 75: (ns/day) (hour/ns) 75: Performance: 694.308 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.1 75: (ns/day) (hour/ns) 75: Performance: 684.054 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 6 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.028 0.014 198.6 75: (ns/day) (hour/ns) 75: Performance: 103.397 0.232 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.7 75: (ns/day) (hour/ns) 75: Performance: 772.391 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.8 75: (ns/day) (hour/ns) 75: Performance: 658.500 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (535 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 191.5 75: (ns/day) (hour/ns) 75: Performance: 574.147 0.042 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 631.888 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.1 75: (ns/day) (hour/ns) 75: Performance: 727.815 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.4 75: (ns/day) (hour/ns) 75: Performance: 678.966 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.9 75: (ns/day) (hour/ns) 75: Performance: 657.972 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.2 75: (ns/day) (hour/ns) 75: Performance: 673.289 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (369 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 3.6%. 75: The balanceable part of the MD step is 66%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.4%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.004 193.2 75: (ns/day) (hour/ns) 75: Performance: 345.965 0.069 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.3%. 75: The balanceable part of the MD step is 69%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.9%. 75: 75: 75: NOTE: 67 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.030 0.015 197.5 75: (ns/day) (hour/ns) 75: Performance: 98.199 0.244 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.6%. 75: The balanceable part of the MD step is 61%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.0%. 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 190.2 75: (ns/day) (hour/ns) 75: Performance: 525.289 0.046 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.6%. 75: The balanceable part of the MD step is 61%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.6%. 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 190.9 75: (ns/day) (hour/ns) 75: Performance: 461.502 0.052 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 3.1%. 75: The balanceable part of the MD step is 61%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.9%. 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 191.4 75: (ns/day) (hour/ns) 75: Performance: 463.918 0.052 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.6%. 75: The balanceable part of the MD step is 65%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.4%. 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 192.8 75: (ns/day) (hour/ns) 75: Performance: 565.555 0.042 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (359 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.0%. 75: The balanceable part of the MD step is 67%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.6%. 75: 75: 75: NOTE: 57 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.063 0.032 198.7 75: (ns/day) (hour/ns) 75: Performance: 45.969 0.522 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.1%. 75: The balanceable part of the MD step is 68%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.4%. 75: 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 192.3 75: (ns/day) (hour/ns) 75: Performance: 442.762 0.054 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.6%. 75: The balanceable part of the MD step is 65%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.4%. 75: 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.7 75: (ns/day) (hour/ns) 75: Performance: 478.753 0.050 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.2%. 75: The balanceable part of the MD step is 62%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.7%. 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.015 0.021 68.3 75: (ns/day) (hour/ns) 75: Performance: 68.607 0.350 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.1%. 75: The balanceable part of the MD step is 61%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.7%. 75: 75: 75: NOTE: 6 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 191.2 75: (ns/day) (hour/ns) 75: Performance: 444.183 0.054 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.3%. 75: The balanceable part of the MD step is 61%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.8%. 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.015 0.021 69.5 75: (ns/day) (hour/ns) 75: Performance: 68.884 0.348 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (499 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.047 0.024 198.2 75: (ns/day) (hour/ns) 75: Performance: 61.700 0.389 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 190.4 75: (ns/day) (hour/ns) 75: Performance: 470.490 0.051 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.9 75: (ns/day) (hour/ns) 75: Performance: 463.743 0.052 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.4 75: (ns/day) (hour/ns) 75: Performance: 449.826 0.053 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 5 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.1 75: (ns/day) (hour/ns) 75: Performance: 488.103 0.049 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.004 162.5 75: (ns/day) (hour/ns) 75: Performance: 339.062 0.071 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (317 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.005 191.9 75: (ns/day) (hour/ns) 75: Performance: 321.912 0.075 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.014 56.8 75: (ns/day) (hour/ns) 75: Performance: 108.564 0.221 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.011 51.0 75: (ns/day) (hour/ns) 75: Performance: 131.792 0.182 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.9 75: (ns/day) (hour/ns) 75: Performance: 464.863 0.052 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 5 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.004 190.7 75: (ns/day) (hour/ns) 75: Performance: 340.139 0.071 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.007 86.4 75: (ns/day) (hour/ns) 75: Performance: 201.442 0.119 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (406 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 11 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.040 0.020 197.6 75: (ns/day) (hour/ns) 75: Performance: 73.388 0.327 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 190.6 75: (ns/day) (hour/ns) 75: Performance: 462.091 0.052 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.017 37.7 75: (ns/day) (hour/ns) 75: Performance: 85.112 0.282 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 6 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.017 36.5 75: (ns/day) (hour/ns) 75: Performance: 84.953 0.283 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.037 0.019 198.1 75: (ns/day) (hour/ns) 75: Performance: 78.729 0.305 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.011 0.019 56.6 75: (ns/day) (hour/ns) 75: Performance: 75.884 0.316 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (511 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.031 0.016 197.0 75: (ns/day) (hour/ns) 75: Performance: 92.982 0.258 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.015 44.5 75: (ns/day) (hour/ns) 75: Performance: 95.867 0.250 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 6 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 190.3 75: (ns/day) (hour/ns) 75: Performance: 457.000 0.053 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 6 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.017 37.3 75: (ns/day) (hour/ns) 75: Performance: 84.619 0.284 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.021 30.6 75: (ns/day) (hour/ns) 75: Performance: 68.600 0.350 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 6 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.012 55.0 75: (ns/day) (hour/ns) 75: Performance: 120.100 0.200 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (453 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.020 0.010 196.1 75: (ns/day) (hour/ns) 75: Performance: 145.961 0.164 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.064 0.032 198.7 75: (ns/day) (hour/ns) 75: Performance: 45.909 0.523 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 59 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.055 0.028 198.5 75: (ns/day) (hour/ns) 75: Performance: 53.175 0.451 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 15 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.055 0.028 198.5 75: (ns/day) (hour/ns) 75: Performance: 52.734 0.455 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 40 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.071 0.036 198.8 75: (ns/day) (hour/ns) 75: Performance: 40.961 0.586 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.024 0.012 196.5 75: (ns/day) (hour/ns) 75: Performance: 120.145 0.200 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (464 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.015 0.012 126.7 75: (ns/day) (hour/ns) 75: Performance: 127.078 0.189 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 48 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.050 0.025 198.8 75: (ns/day) (hour/ns) 75: Performance: 57.867 0.415 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 190.9 75: (ns/day) (hour/ns) 75: Performance: 506.420 0.047 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 20 % of the run time was spent in domain decomposition, 75: 0 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.673 0.337 199.9 75: (ns/day) (hour/ns) 75: Performance: 4.360 5.504 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.047 0.024 198.2 75: (ns/day) (hour/ns) 75: Performance: 61.531 0.390 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI threads 75: Using 1 OpenMP thread per tMPI thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Writing final coordinates. 75: 75: NOTE: 62 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.032 0.016 196.7 75: (ns/day) (hour/ns) 75: Performance: 90.939 0.264 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (1044 ms) 75: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (10974 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 22 tests from 1 test suite ran. (11137 ms total) 75: [ PASSED ] 22 tests. 75/81 Test #75: MdrunMpiCoordinationCouplingTestsTwoRanks ...... Passed 11.16 sec test 76 Start 76: MdrunMpiCoordinationConstraintsTestsOneRank 76: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-mpi-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationConstraintsTestsOneRank.xml" 76: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 76: Test timeout computed to be: 1920 76: [==========] Running 10 tests from 1 test suite. 76: [----------] Global test environment set-up. 76: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.007 0.007 98.8 76: (ns/day) (hour/ns) 76: Performance: 206.482 0.116 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.005 37.7 76: (ns/day) (hour/ns) 76: Performance: 272.593 0.088 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 97.7 76: (ns/day) (hour/ns) 76: Performance: 455.598 0.053 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 97.4 76: (ns/day) (hour/ns) 76: Performance: 390.331 0.061 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 97.1 76: (ns/day) (hour/ns) 76: Performance: 461.987 0.052 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.4 76: (ns/day) (hour/ns) 76: Performance: 723.074 0.033 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (3895 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.005 97.9 76: (ns/day) (hour/ns) 76: Performance: 320.247 0.075 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 97.6 76: (ns/day) (hour/ns) 76: Performance: 391.746 0.061 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 97.0 76: (ns/day) (hour/ns) 76: Performance: 502.372 0.048 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.010 0.010 99.2 76: (ns/day) (hour/ns) 76: Performance: 143.567 0.167 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.013 0.013 99.2 76: (ns/day) (hour/ns) 76: Performance: 114.917 0.209 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.7 76: (ns/day) (hour/ns) 76: Performance: 763.868 0.031 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (4634 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.011 0.011 99.2 76: (ns/day) (hour/ns) 76: Performance: 130.521 0.184 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.6 76: (ns/day) (hour/ns) 76: Performance: 733.753 0.033 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.6 76: (ns/day) (hour/ns) 76: Performance: 856.233 0.028 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.3 76: (ns/day) (hour/ns) 76: Performance: 762.450 0.031 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.7 76: (ns/day) (hour/ns) 76: Performance: 806.677 0.030 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.006 0.006 98.6 76: (ns/day) (hour/ns) 76: Performance: 229.513 0.105 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (5548 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.011 0.011 99.1 76: (ns/day) (hour/ns) 76: Performance: 132.460 0.181 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.0 76: (ns/day) (hour/ns) 76: Performance: 740.011 0.032 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.4 76: (ns/day) (hour/ns) 76: Performance: 871.002 0.028 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 96.5 76: (ns/day) (hour/ns) 76: Performance: 520.716 0.046 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.6 76: (ns/day) (hour/ns) 76: Performance: 749.099 0.032 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.009 0.009 99.0 76: (ns/day) (hour/ns) 76: Performance: 157.142 0.153 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (6871 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 97.6 76: (ns/day) (hour/ns) 76: Performance: 352.881 0.068 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 97.8 76: (ns/day) (hour/ns) 76: Performance: 391.596 0.061 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.006 0.006 98.4 76: (ns/day) (hour/ns) 76: Performance: 232.528 0.103 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.3 76: (ns/day) (hour/ns) 76: Performance: 672.334 0.036 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.8 76: (ns/day) (hour/ns) 76: Performance: 757.016 0.032 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 97.5 76: (ns/day) (hour/ns) 76: Performance: 371.725 0.065 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (4531 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.011 0.011 99.4 76: (ns/day) (hour/ns) 76: Performance: 131.769 0.182 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.8 76: (ns/day) (hour/ns) 76: Performance: 624.933 0.038 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.005 0.005 98.5 76: (ns/day) (hour/ns) 76: Performance: 267.503 0.090 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.004 97.9 76: (ns/day) (hour/ns) 76: Performance: 411.145 0.058 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.010 0.011 99.2 76: (ns/day) (hour/ns) 76: Performance: 138.833 0.173 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.6 76: (ns/day) (hour/ns) 76: Performance: 662.928 0.036 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (4118 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.005 0.005 98.3 76: (ns/day) (hour/ns) 76: Performance: 310.326 0.077 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.007 0.007 98.9 76: (ns/day) (hour/ns) 76: Performance: 201.518 0.119 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.007 0.007 98.8 76: (ns/day) (hour/ns) 76: Performance: 222.839 0.108 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.010 17.6 76: (ns/day) (hour/ns) 76: Performance: 148.814 0.161 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.006 0.006 98.7 76: (ns/day) (hour/ns) 76: Performance: 233.515 0.103 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.6 76: (ns/day) (hour/ns) 76: Performance: 759.817 0.032 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (4819 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.005 99.0 76: (ns/day) (hour/ns) 76: Performance: 323.765 0.074 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 98.5 76: (ns/day) (hour/ns) 76: Performance: 543.886 0.044 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 98.4 76: (ns/day) (hour/ns) 76: Performance: 639.198 0.038 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.006 0.006 99.1 76: (ns/day) (hour/ns) 76: Performance: 252.019 0.095 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: NOTE: 39 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.8 76: (ns/day) (hour/ns) 76: Performance: 344.552 0.070 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.005 0.005 98.6 76: (ns/day) (hour/ns) 76: Performance: 285.954 0.084 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (3594 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.005 0.005 98.7 76: (ns/day) (hour/ns) 76: Performance: 320.131 0.075 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.005 50.2 76: (ns/day) (hour/ns) 76: Performance: 297.656 0.081 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 97.8 76: (ns/day) (hour/ns) 76: Performance: 646.035 0.037 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.015 0.015 99.5 76: (ns/day) (hour/ns) 76: Performance: 100.293 0.239 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 97.8 76: (ns/day) (hour/ns) 76: Performance: 596.783 0.040 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.4 76: (ns/day) (hour/ns) 76: Performance: 393.724 0.061 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (4941 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.012 0.012 99.4 76: (ns/day) (hour/ns) 76: Performance: 126.449 0.190 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 97.7 76: (ns/day) (hour/ns) 76: Performance: 588.798 0.041 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 97.9 76: (ns/day) (hour/ns) 76: Performance: 676.097 0.035 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.6 76: (ns/day) (hour/ns) 76: Performance: 352.638 0.068 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.005 0.005 98.8 76: (ns/day) (hour/ns) 76: Performance: 315.120 0.076 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 76: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 76: 76: Using 1 MPI thread 76: Using 1 OpenMP thread 76: 76: 76: NOTE: Thread affinity was not set. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.006 0.006 99.0 76: (ns/day) (hour/ns) 76: Performance: 226.509 0.106 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (5122 ms) 76: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (48076 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 10 tests from 1 test suite ran. (48239 ms total) 76: [ PASSED ] 10 tests. 76/81 Test #76: MdrunMpiCoordinationConstraintsTestsOneRank .... Passed 48.30 sec test 77 Start 77: MdrunMpiCoordinationConstraintsTestsTwoRanks 77: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-mpi-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationConstraintsTestsTwoRanks.xml" 77: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 77: Test timeout computed to be: 1920 77: [==========] Running 10 tests from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 0.0%. 77: The balanceable part of the MD step is 43%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.0%. 77: 77: 77: NOTE: 14 % of the run time was spent in domain decomposition, 77: 0 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: NOTE: 33 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 1.776 0.920 193.1 77: (ns/day) (hour/ns) 77: Performance: 1.597 15.032 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.5%. 77: The balanceable part of the MD step is 59%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.9%. 77: 77: 77: NOTE: 25 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 192.4 77: (ns/day) (hour/ns) 77: Performance: 567.274 0.042 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 0.9%. 77: The balanceable part of the MD step is 56%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.5%. 77: 77: 77: NOTE: 45 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.021 0.010 197.8 77: (ns/day) (hour/ns) 77: Performance: 140.717 0.171 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 3.6%. 77: The balanceable part of the MD step is 53%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.9%. 77: 77: 77: NOTE: 27 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 192.1 77: (ns/day) (hour/ns) 77: Performance: 605.107 0.040 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB got disabled because it was unsuitable to use. 77: Average load imbalance: 4.0%. 77: The balanceable part of the MD step is 53%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 2.1%. 77: 77: 77: NOTE: 28 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 191.5 77: (ns/day) (hour/ns) 77: Performance: 558.000 0.043 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.5%. 77: The balanceable part of the MD step is 54%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.4%. 77: 77: 77: NOTE: 28 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 191.2 77: (ns/day) (hour/ns) 77: Performance: 616.029 0.039 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (6404 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.8%. 77: The balanceable part of the MD step is 8%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.1%. 77: 77: 77: NOTE: 90 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.071 0.036 198.9 77: (ns/day) (hour/ns) 77: Performance: 41.043 0.585 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 0.1%. 77: The balanceable part of the MD step is 46%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.0%. 77: 77: 77: NOTE: 17 % of the run time was spent in domain decomposition, 77: 0 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: NOTE: 40 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 1.488 0.760 195.8 77: (ns/day) (hour/ns) 77: Performance: 1.933 12.415 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB got disabled because it was unsuitable to use. 77: Average load imbalance: 5.1%. 77: The balanceable part of the MD step is 56%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 2.9%. 77: 77: 77: NOTE: 26 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 190.0 77: (ns/day) (hour/ns) 77: Performance: 607.105 0.040 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.4%. 77: The balanceable part of the MD step is 56%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.4%. 77: 77: 77: NOTE: 9 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.015 35.7 77: (ns/day) (hour/ns) 77: Performance: 98.582 0.243 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.3%. 77: The balanceable part of the MD step is 27%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.6%. 77: 77: 77: NOTE: 33 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.009 0.004 194.2 77: (ns/day) (hour/ns) 77: Performance: 327.639 0.073 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.8%. 77: The balanceable part of the MD step is 61%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.7%. 77: 77: 77: NOTE: 29 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 191.4 77: (ns/day) (hour/ns) 77: Performance: 681.972 0.035 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (6723 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.012 0.006 195.9 77: (ns/day) (hour/ns) 77: Performance: 237.581 0.101 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 191.5 77: (ns/day) (hour/ns) 77: Performance: 578.324 0.041 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.003 0.002 191.1 77: (ns/day) (hour/ns) 77: Performance: 808.583 0.030 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 192.2 77: (ns/day) (hour/ns) 77: Performance: 634.524 0.038 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 191.9 77: (ns/day) (hour/ns) 77: Performance: 606.208 0.040 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 191.2 77: (ns/day) (hour/ns) 77: Performance: 599.105 0.040 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (4236 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.025 0.012 197.6 77: (ns/day) (hour/ns) 77: Performance: 117.856 0.204 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 192.6 77: (ns/day) (hour/ns) 77: Performance: 521.819 0.046 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 189.5 77: (ns/day) (hour/ns) 77: Performance: 591.313 0.041 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 191.5 77: (ns/day) (hour/ns) 77: Performance: 571.882 0.042 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 190.9 77: (ns/day) (hour/ns) 77: Performance: 708.644 0.034 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 190.8 77: (ns/day) (hour/ns) 77: Performance: 610.201 0.039 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (4274 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 15 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.019 0.010 196.9 77: (ns/day) (hour/ns) 77: Performance: 148.546 0.162 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 192.4 77: (ns/day) (hour/ns) 77: Performance: 667.960 0.036 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 191.0 77: (ns/day) (hour/ns) 77: Performance: 531.154 0.045 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 191.7 77: (ns/day) (hour/ns) 77: Performance: 566.856 0.042 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 191.3 77: (ns/day) (hour/ns) 77: Performance: 681.293 0.035 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 190.6 77: (ns/day) (hour/ns) 77: Performance: 588.095 0.041 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (4937 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.010 0.005 195.6 77: (ns/day) (hour/ns) 77: Performance: 292.470 0.082 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.006 0.015 38.8 77: (ns/day) (hour/ns) 77: Performance: 97.597 0.246 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 193.4 77: (ns/day) (hour/ns) 77: Performance: 641.461 0.037 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 192.1 77: (ns/day) (hour/ns) 77: Performance: 570.135 0.042 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.011 0.005 196.2 77: (ns/day) (hour/ns) 77: Performance: 269.598 0.089 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 192.5 77: (ns/day) (hour/ns) 77: Performance: 551.308 0.044 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (5882 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.007 0.004 193.8 77: (ns/day) (hour/ns) 77: Performance: 387.959 0.062 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.031 0.016 198.4 77: (ns/day) (hour/ns) 77: Performance: 93.270 0.257 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 192.7 77: (ns/day) (hour/ns) 77: Performance: 554.459 0.043 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.013 0.011 118.0 77: (ns/day) (hour/ns) 77: Performance: 132.658 0.181 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 191.4 77: (ns/day) (hour/ns) 77: Performance: 542.855 0.044 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 191.6 77: (ns/day) (hour/ns) 77: Performance: 516.222 0.046 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (4406 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.4%. 77: The balanceable part of the MD step is 67%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.9%. 77: 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.009 0.005 192.5 77: (ns/day) (hour/ns) 77: Performance: 322.620 0.074 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.3%. 77: The balanceable part of the MD step is 69%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.9%. 77: 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.009 0.005 192.5 77: (ns/day) (hour/ns) 77: Performance: 308.076 0.078 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB got disabled because it was unsuitable to use. 77: Average load imbalance: 8.2%. 77: The balanceable part of the MD step is 61%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 4.9%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.031 0.016 197.4 77: (ns/day) (hour/ns) 77: Performance: 92.415 0.260 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB got disabled because it was unsuitable to use. 77: Average load imbalance: 8.0%. 77: The balanceable part of the MD step is 35%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 2.8%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.008 0.004 194.7 77: (ns/day) (hour/ns) 77: Performance: 360.279 0.067 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB got disabled because it was unsuitable to use. 77: Average load imbalance: 6.6%. 77: The balanceable part of the MD step is 59%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 3.9%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.006 0.003 193.1 77: (ns/day) (hour/ns) 77: Performance: 505.713 0.047 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.1%. 77: The balanceable part of the MD step is 62%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.7%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.007 0.005 128.0 77: (ns/day) (hour/ns) 77: Performance: 283.467 0.085 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (5169 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.012 0.006 194.7 77: (ns/day) (hour/ns) 77: Performance: 241.924 0.099 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.009 0.007 120.6 77: (ns/day) (hour/ns) 77: Performance: 203.858 0.118 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 7 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.006 0.003 191.1 77: (ns/day) (hour/ns) 77: Performance: 495.862 0.048 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 10 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.007 0.004 192.6 77: (ns/day) (hour/ns) 77: Performance: 404.584 0.059 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.006 0.021 29.2 77: (ns/day) (hour/ns) 77: Performance: 69.184 0.347 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.007 0.004 190.0 77: (ns/day) (hour/ns) 77: Performance: 388.032 0.062 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (4148 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.010 0.005 192.4 77: (ns/day) (hour/ns) 77: Performance: 292.644 0.082 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.020 0.010 196.2 77: (ns/day) (hour/ns) 77: Performance: 142.539 0.168 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.003 190.6 77: (ns/day) (hour/ns) 77: Performance: 536.053 0.045 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.006 0.003 190.3 77: (ns/day) (hour/ns) 77: Performance: 504.656 0.048 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.025 0.013 196.8 77: (ns/day) (hour/ns) 77: Performance: 117.203 0.205 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generating 1-4 interactions: fudge = 0.5 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 77: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 77: 77: Using 2 MPI threads 77: Using 1 OpenMP thread per tMPI thread 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.008 0.004 192.0 77: (ns/day) (hour/ns) 77: Performance: 354.587 0.068 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (5544 ms) 77: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (51728 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 10 tests from 1 test suite ran. (51867 ms total) 77: [ PASSED ] 10 tests. 77/81 Test #77: MdrunMpiCoordinationConstraintsTestsTwoRanks ... Passed 51.91 sec test 78 Start 78: MdrunFEPTests 78: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunFEPTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 10 tests from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 10 tests from EquivalentToReference/FreeEnergyReferenceTest 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to 1575477166 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.92 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.790 0.395 199.9 78: (ns/day) (hour/ns) 78: Performance: 4.591 5.228 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_energy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (double precision) 78: 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d (952 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -25231378 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.92 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.737 0.369 199.9 78: (ns/day) (hour/ns) 78: Performance: 4.920 4.878 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_energy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d (519 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: With PME there is a minor soft core effect present at the cut-off, 78: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 78: energy conservation, but usually other effects dominate. With a common 78: sigma value of 0.34 nm the fraction of the particle-particle potential at 78: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 4 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -125837809 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.92 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.525 0.263 199.9 78: (ns/day) (hour/ns) 78: Performance: 6.907 3.475 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_energy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d (414 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 78: and vdw_modifier=Force-switch 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 4 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 100 steps, 0.1 ps. 78: Setting the LD random seed to 1332715518 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.92 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 3.457 1.729 200.0 78: (ns/day) (hour/ns) 78: Performance: 5.048 4.755 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_energy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d (1876 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: WARNING 2 [file topol.top, line 72]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 3 [file topol.top, line 73]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 4 [file topol.top, line 98]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 5 [file topol.top, line 99]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 6 [file topol.top, line 100]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 7 [file topol.top, line 101]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 8 [file topol.top, line 111]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 9 [file topol.top, line 112]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 10 [file topol.top, line 113]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 11 [file topol.top, line 114]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 2 notes 78: 78: There were 11 warnings 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -1077977539 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.92 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.225 0.612 200.0 78: (ns/day) (hour/ns) 78: Performance: 2.962 8.102 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_energy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d (761 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: WARNING 2 [file topol.top, line 72]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 3 [file topol.top, line 73]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 4 [file topol.top, line 98]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 5 [file topol.top, line 99]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 6 [file topol.top, line 100]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 7 [file topol.top, line 101]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 8 [file topol.top, line 111]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 9 [file topol.top, line 112]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 10 [file topol.top, line 113]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 11 [file topol.top, line 114]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: Removing center of mass motion in the presence of position restraints 78: might cause artifacts. When you are using position restraints to 78: equilibrate a macro-molecule, the artifacts are usually negligible. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There were 11 warnings 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -2097665 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.92 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.354 0.677 200.0 78: (ns/day) (hour/ns) 78: Performance: 2.679 8.960 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_energy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d (823 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 2 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -1287656705 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.331 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.86 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.172 0.086 199.7 78: (ns/day) (hour/ns) 78: Performance: 21.035 1.141 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_energy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d (238 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There was 1 note 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.232 0.116 199.8 78: (ns/day) (hour/ns) 78: Performance: 15.604 1.538 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_energy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 78: Setting the LD random seed to -270074009 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between excluded atoms is 0.331 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.86 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (266 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: With PME there is a minor soft core effect present at the cut-off, 78: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 78: energy conservation, but usually other effects dominate. With a common 78: sigma value of 0.34 nm the fraction of the particle-particle potential at 78: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -1350573321 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.92 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.428 0.214 199.9 78: (ns/day) (hour/ns) 78: Performance: 8.466 2.835 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_energy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d (284 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: With PME there is a minor soft core effect present at the cut-off, 78: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 78: energy conservation, but usually other effects dominate. With a common 78: sigma value of 0.34 nm the fraction of the particle-particle potential at 78: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI thread 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to 2136964799 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.172 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.86 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.148 0.074 199.6 78: (ns/day) (hour/ns) 78: Performance: 24.552 0.978 78: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_energy.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d (131 ms) 78: [----------] 10 tests from EquivalentToReference/FreeEnergyReferenceTest (6280 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 10 tests from 1 test suite ran. (6452 ms total) 78: [ PASSED ] 10 tests. 78/81 Test #78: MdrunFEPTests .................................. Passed 6.51 sec test 79 Start 79: MdrunPullTests 79: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunPullTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 4 tests from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 4 tests from PullTest/PullIntegrationTest 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1293.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.122 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.575 nm 0.600 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 13 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.124 0.062 199.6 79: (ns/day) (hour/ns) 79: Performance: 29.302 0.819 79: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (819 ms) 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1293.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.122 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.301 nm 0.400 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.287 0.144 199.8 79: (ns/day) (hour/ns) 79: Performance: 12.611 1.903 79: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (793 ms) 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Pull group 3 'r_3' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1292.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.357 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.575 nm 0.500 nm 79: 1 3 2 79: 3 3 8 0.331 nm 0.400 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.782 nm, buffer size 0.082 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.111 0.056 199.6 79: (ns/day) (hour/ns) 79: Performance: 32.643 0.735 79: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (859 ms) 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1293.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.122 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.575 nm 0.000 nm 79: 1 3 2 79: 2 3 5 0.050 nm 0.000 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.113 0.057 199.6 79: (ns/day) (hour/ns) 79: Performance: 31.935 0.752 79: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (625 ms) 79: [----------] 4 tests from PullTest/PullIntegrationTest (3098 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 4 tests from 1 test suite ran. (3253 ms total) 79: [ PASSED ] 4 tests. 79/81 Test #79: MdrunPullTests ................................. Passed 3.32 sec test 80 Start 80: MdrunSimulatorComparison 80: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunSimulatorComparison.xml" 80: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 94 tests from 4 test suites. 80: [----------] Global test environment set-up. 80: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 59 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.096 0.048 199.8 80: (ns/day) (hour/ns) 80: Performance: 30.549 0.786 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.113 0.057 199.6 80: (ns/day) (hour/ns) 80: Performance: 25.853 0.928 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 80: 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (145 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.002 196.3 80: (ns/day) (hour/ns) 80: Performance: 590.491 0.041 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.002 192.8 80: (ns/day) (hour/ns) 80: Performance: 603.093 0.040 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (66 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.002 196.0 80: (ns/day) (hour/ns) 80: Performance: 587.899 0.041 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 192.2 80: (ns/day) (hour/ns) 80: Performance: 631.402 0.038 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 (78 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.044 0.022 199.5 80: (ns/day) (hour/ns) 80: Performance: 65.899 0.364 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.017 0.009 189.5 80: (ns/day) (hour/ns) 80: Performance: 164.836 0.146 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 (77 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.007 0.003 195.2 80: (ns/day) (hour/ns) 80: Performance: 431.263 0.056 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.002 192.0 80: (ns/day) (hour/ns) 80: Performance: 620.465 0.039 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 (24 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 195.6 80: (ns/day) (hour/ns) 80: Performance: 568.740 0.042 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 193.5 80: (ns/day) (hour/ns) 80: Performance: 645.088 0.037 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 (20 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: 80: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: 80: There were 2 warnings 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.009 0.005 197.4 80: (ns/day) (hour/ns) 80: Performance: 319.715 0.075 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.008 0.004 195.4 80: (ns/day) (hour/ns) 80: Performance: 366.266 0.066 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 (22 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 196.0 80: (ns/day) (hour/ns) 80: Performance: 547.025 0.044 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.013 0.006 196.9 80: (ns/day) (hour/ns) 80: Performance: 227.976 0.105 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 (22 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.007 0.004 196.0 80: (ns/day) (hour/ns) 80: Performance: 384.604 0.062 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: NOTE: 37 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.008 0.004 195.2 80: (ns/day) (hour/ns) 80: Performance: 379.300 0.063 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 (21 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.007 0.004 196.4 80: (ns/day) (hour/ns) 80: Performance: 394.859 0.061 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.007 0.003 194.8 80: (ns/day) (hour/ns) 80: Performance: 439.540 0.055 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 (21 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 196.3 80: (ns/day) (hour/ns) 80: Performance: 509.603 0.047 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.007 0.003 194.4 80: (ns/day) (hour/ns) 80: Performance: 429.429 0.056 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 (21 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.008 0.004 196.7 80: (ns/day) (hour/ns) 80: Performance: 349.161 0.069 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 192.6 80: (ns/day) (hour/ns) 80: Performance: 557.823 0.043 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 (21 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 80: Andersen temperature control methods assume nsttcouple = 1; there is no 80: need for larger nsttcouple > 1, since no global parameters are computed. 80: nsttcouple has been reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.009 0.004 197.3 80: (ns/day) (hour/ns) 80: Performance: 336.442 0.071 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.008 0.004 195.1 80: (ns/day) (hour/ns) 80: Performance: 373.460 0.064 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 (22 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 80: Andersen temperature control methods assume nsttcouple = 1; there is no 80: need for larger nsttcouple > 1, since no global parameters are computed. 80: nsttcouple has been reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 193.7 80: (ns/day) (hour/ns) 80: Performance: 512.017 0.047 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.002 193.0 80: (ns/day) (hour/ns) 80: Performance: 602.267 0.040 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 (21 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 80: Andersen temperature control methods assume nsttcouple = 1; there is no 80: need for larger nsttcouple > 1, since no global parameters are computed. 80: nsttcouple has been reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.008 0.004 196.7 80: (ns/day) (hour/ns) 80: Performance: 370.451 0.065 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 192.7 80: (ns/day) (hour/ns) 80: Performance: 685.729 0.035 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 (20 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 80: Center of mass removal not necessary for Andersen. All velocities of 80: coupled groups are rerandomized periodically, so flying ice cube errors 80: will not occur. 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 80: Andersen temperature control methods assume nsttcouple = 1; there is no 80: need for larger nsttcouple > 1, since no global parameters are computed. 80: nsttcouple has been reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 196.0 80: (ns/day) (hour/ns) 80: Performance: 523.949 0.046 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 192.5 80: (ns/day) (hour/ns) 80: Performance: 512.103 0.047 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 (23 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 80: Center of mass removal not necessary for Andersen. All velocities of 80: coupled groups are rerandomized periodically, so flying ice cube errors 80: will not occur. 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 80: Andersen temperature control methods assume nsttcouple = 1; there is no 80: need for larger nsttcouple > 1, since no global parameters are computed. 80: nsttcouple has been reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 194.4 80: (ns/day) (hour/ns) 80: Performance: 543.550 0.044 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.007 197.7 80: (ns/day) (hour/ns) 80: Performance: 199.211 0.120 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 (26 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 80: Center of mass removal not necessary for Andersen. All velocities of 80: coupled groups are rerandomized periodically, so flying ice cube errors 80: will not occur. 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 80: Andersen temperature control methods assume nsttcouple = 1; there is no 80: need for larger nsttcouple > 1, since no global parameters are computed. 80: nsttcouple has been reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 195.7 80: (ns/day) (hour/ns) 80: Performance: 522.350 0.046 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.008 0.004 195.8 80: (ns/day) (hour/ns) 80: Performance: 344.206 0.070 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 (20 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 80: NVE simulation: will use the initial temperature of 398.997 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 196.5 80: (ns/day) (hour/ns) 80: Performance: 481.899 0.050 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 197.2 80: (ns/day) (hour/ns) 80: Performance: 210.475 0.114 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 (1338 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 80: NVE simulation: will use the initial temperature of 398.997 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.033 0.016 198.5 80: (ns/day) (hour/ns) 80: Performance: 89.379 0.269 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.023 0.012 194.2 80: (ns/day) (hour/ns) 80: Performance: 124.784 0.192 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 (1313 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.034 0.017 199.2 80: (ns/day) (hour/ns) 80: Performance: 87.013 0.276 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.018 0.009 197.8 80: (ns/day) (hour/ns) 80: Performance: 157.725 0.152 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 (775 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 196.2 80: (ns/day) (hour/ns) 80: Performance: 570.637 0.042 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.002 193.9 80: (ns/day) (hour/ns) 80: Performance: 625.060 0.038 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 (779 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 198.4 80: (ns/day) (hour/ns) 80: Performance: 179.499 0.134 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 193.0 80: (ns/day) (hour/ns) 80: Performance: 646.510 0.037 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 (774 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.015 199.2 80: (ns/day) (hour/ns) 80: Performance: 95.555 0.251 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.010 198.7 80: (ns/day) (hour/ns) 80: Performance: 141.097 0.170 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 (577 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: 80: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: 80: There were 2 warnings 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 198.2 80: (ns/day) (hour/ns) 80: Performance: 179.478 0.134 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 192.2 80: (ns/day) (hour/ns) 80: Performance: 568.740 0.042 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 (844 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.029 0.014 199.0 80: (ns/day) (hour/ns) 80: Performance: 102.174 0.235 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 193.9 80: (ns/day) (hour/ns) 80: Performance: 443.943 0.054 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 (653 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.048 0.024 199.1 80: (ns/day) (hour/ns) 80: Performance: 61.168 0.392 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.038 0.019 199.1 80: (ns/day) (hour/ns) 80: Performance: 77.103 0.311 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 (982 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 197.9 80: (ns/day) (hour/ns) 80: Performance: 182.018 0.132 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 192.5 80: (ns/day) (hour/ns) 80: Performance: 538.325 0.045 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 (728 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 80: Andersen temperature control methods assume nsttcouple = 1; there is no 80: need for larger nsttcouple > 1, since no global parameters are computed. 80: nsttcouple has been reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.024 0.012 198.8 80: (ns/day) (hour/ns) 80: Performance: 120.763 0.199 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 193.6 80: (ns/day) (hour/ns) 80: Performance: 550.988 0.044 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 (1106 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 80: Andersen temperature control methods assume nsttcouple = 1; there is no 80: need for larger nsttcouple > 1, since no global parameters are computed. 80: nsttcouple has been reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.022 0.011 198.6 80: (ns/day) (hour/ns) 80: Performance: 135.582 0.177 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 193.1 80: (ns/day) (hour/ns) 80: Performance: 552.916 0.043 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 (631 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 80: Andersen temperature control methods assume nsttcouple = 1; there is no 80: need for larger nsttcouple > 1, since no global parameters are computed. 80: nsttcouple has been reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 196.1 80: (ns/day) (hour/ns) 80: Performance: 568.373 0.042 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.012 0.006 195.8 80: (ns/day) (hour/ns) 80: Performance: 236.400 0.102 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 (1267 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 80: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 (0 ms) 80: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (12457 ms total) 80: 80: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 191.1 80: (ns/day) (hour/ns) 80: Performance: 640.661 0.037 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: NOTE: 63 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.077 0.039 199.7 80: (ns/day) (hour/ns) 80: Performance: 38.105 0.630 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (121 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 191.4 80: (ns/day) (hour/ns) 80: Performance: 666.515 0.036 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.013 0.007 197.8 80: (ns/day) (hour/ns) 80: Performance: 216.876 0.111 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (112 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 191.2 80: (ns/day) (hour/ns) 80: Performance: 670.942 0.036 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 196.7 80: (ns/day) (hour/ns) 80: Performance: 504.140 0.048 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (118 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 191.5 80: (ns/day) (hour/ns) 80: Performance: 700.944 0.034 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.077 0.039 199.7 80: (ns/day) (hour/ns) 80: Performance: 37.867 0.634 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (70 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.002 191.5 80: (ns/day) (hour/ns) 80: Performance: 615.014 0.039 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.045 0.023 199.3 80: (ns/day) (hour/ns) 80: Performance: 64.663 0.371 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (126 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.011 197.8 80: (ns/day) (hour/ns) 80: Performance: 138.534 0.173 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.013 0.006 198.2 80: (ns/day) (hour/ns) 80: Performance: 229.453 0.105 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (62 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 191.2 80: (ns/day) (hour/ns) 80: Performance: 715.101 0.034 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.101 0.051 199.7 80: (ns/day) (hour/ns) 80: Performance: 29.028 0.827 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (109 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 192.0 80: (ns/day) (hour/ns) 80: Performance: 667.887 0.036 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.022 0.011 198.3 80: (ns/day) (hour/ns) 80: Performance: 130.948 0.183 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 (76 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.067 0.034 199.3 80: (ns/day) (hour/ns) 80: Performance: 43.663 0.550 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.030 0.015 199.0 80: (ns/day) (hour/ns) 80: Performance: 98.827 0.243 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 (69 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: 80: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: 80: There were 2 warnings 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.010 198.1 80: (ns/day) (hour/ns) 80: Performance: 141.376 0.170 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.025 0.012 198.9 80: (ns/day) (hour/ns) 80: Performance: 118.965 0.202 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 (47 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 191.8 80: (ns/day) (hour/ns) 80: Performance: 714.686 0.034 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 195.3 80: (ns/day) (hour/ns) 80: Performance: 570.531 0.042 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 (77 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 191.0 80: (ns/day) (hour/ns) 80: Performance: 769.497 0.031 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.008 198.2 80: (ns/day) (hour/ns) 80: Performance: 190.489 0.126 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 (38 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.037 0.018 199.0 80: (ns/day) (hour/ns) 80: Performance: 79.849 0.301 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 195.8 80: (ns/day) (hour/ns) 80: Performance: 540.119 0.044 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 (61 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 193.0 80: (ns/day) (hour/ns) 80: Performance: 765.957 0.031 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.045 0.023 199.4 80: (ns/day) (hour/ns) 80: Performance: 64.422 0.373 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 (53 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 191.4 80: (ns/day) (hour/ns) 80: Performance: 688.488 0.035 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 195.6 80: (ns/day) (hour/ns) 80: Performance: 571.113 0.042 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 (62 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 398.997 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 193.0 80: (ns/day) (hour/ns) 80: Performance: 656.290 0.037 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 197.3 80: (ns/day) (hour/ns) 80: Performance: 487.157 0.049 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 (919 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 398.997 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.010 0.005 196.1 80: (ns/day) (hour/ns) 80: Performance: 291.944 0.082 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 196.8 80: (ns/day) (hour/ns) 80: Performance: 533.570 0.045 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 (604 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 398.997 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.026 0.013 198.2 80: (ns/day) (hour/ns) 80: Performance: 111.575 0.215 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 197.1 80: (ns/day) (hour/ns) 80: Performance: 504.181 0.048 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 (830 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 (0 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.055 0.027 199.2 80: (ns/day) (hour/ns) 80: Performance: 53.525 0.448 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 196.3 80: (ns/day) (hour/ns) 80: Performance: 507.253 0.047 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 (1273 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.031 0.024 130.4 80: (ns/day) (hour/ns) 80: Performance: 61.830 0.388 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.018 0.009 198.4 80: (ns/day) (hour/ns) 80: Performance: 163.065 0.147 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 (1406 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 196.9 80: (ns/day) (hour/ns) 80: Performance: 200.874 0.119 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.022 0.011 198.8 80: (ns/day) (hour/ns) 80: Performance: 134.393 0.179 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 (1102 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.027 0.013 198.1 80: (ns/day) (hour/ns) 80: Performance: 109.000 0.220 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 195.6 80: (ns/day) (hour/ns) 80: Performance: 494.192 0.049 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 (649 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.018 0.009 197.8 80: (ns/day) (hour/ns) 80: Performance: 157.689 0.152 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 196.3 80: (ns/day) (hour/ns) 80: Performance: 541.734 0.044 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 (636 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.024 0.012 198.2 80: (ns/day) (hour/ns) 80: Performance: 122.154 0.196 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.029 0.014 198.9 80: (ns/day) (hour/ns) 80: Performance: 101.747 0.236 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 (961 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: 80: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: 80: There were 2 warnings 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.027 0.014 198.4 80: (ns/day) (hour/ns) 80: Performance: 107.050 0.224 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.036 0.018 199.1 80: (ns/day) (hour/ns) 80: Performance: 81.419 0.295 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 (833 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 80: The Berendsen thermostat does not generate the correct kinetic energy 80: distribution, and should not be used for new production simulations (in 80: our opinion). We would recommend the V-rescale thermostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 3 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.032 0.016 198.5 80: (ns/day) (hour/ns) 80: Performance: 92.151 0.260 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: NOTE: 58 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.015 0.007 198.4 80: (ns/day) (hour/ns) 80: Performance: 197.373 0.122 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 (1010 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.048 0.024 199.1 80: (ns/day) (hour/ns) 80: Performance: 61.390 0.391 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: NOTE: 59 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.014 0.007 198.1 80: (ns/day) (hour/ns) 80: Performance: 206.822 0.116 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 (1392 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.025 0.013 198.4 80: (ns/day) (hour/ns) 80: Performance: 114.971 0.209 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.004 168.7 80: (ns/day) (hour/ns) 80: Performance: 416.904 0.058 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 (696 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: For isotropic scaling we would recommend the C-rescale barostat that also 80: ensures fast relaxation without oscillations, and for anisotropic scaling 80: you likely want to use the Parrinello-Rahman barostat. 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: 80: There was 1 warning 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.016 0.008 197.3 80: (ns/day) (hour/ns) 80: Performance: 178.754 0.134 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.022 0.011 198.5 80: (ns/day) (hour/ns) 80: Performance: 130.657 0.184 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 (685 ms) 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Number of degrees of freedom in T-Coupling group System is 27.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 80: You are using a plain Coulomb cut-off, which might produce artifacts. 80: You might want to consider using PME electrostatics. 80: 80: 80: 80: There were 4 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 330891 of the 330891 non-bonded parameter combinations 80: 80: Generated 330891 of the 330891 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.029 0.015 198.6 80: (ns/day) (hour/ns) 80: Performance: 100.036 0.240 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 80: 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.011 0.006 197.7 80: (ns/day) (hour/ns) 80: Performance: 253.919 0.095 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 (1288 ms) 80: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (15500 ms total) 80: 80: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest 80: [ RUN ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 2573.591 K for 80: determining the Verlet buffer size 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 196.6 80: (ns/day) (hour/ns) 80: Performance: 462.403 0.052 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 193.0 80: (ns/day) (hour/ns) 80: Performance: 522.173 0.046 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 (61 ms) 80: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (61 ms total) 80: 80: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest 80: [ RUN ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Generating 1-4 interactions: fudge = 0.5 80: Pull group 1 'FirstWaterMolecule' has 3 atoms 80: Pull group 2 'SecondWaterMolecule' has 3 atoms 80: Number of degrees of freedom in T-Coupling group System is 9.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 2573.591 K for 80: determining the Verlet buffer size 80: 80: Pull group natoms pbc atom distance at start reference at t=0 80: 1 3 2 80: 2 3 5 1.112 nm 1.000 nm 80: 80: There were 3 notes 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: Generated 3 of the 3 non-bonded parameter combinations 80: 80: Generated 3 of the 3 1-4 parameter combinations 80: 80: Excluding 2 bonded neighbours molecule type 'SOL' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 191.8 80: (ns/day) (hour/ns) 80: Performance: 645.291 0.037 80: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 80: log). 80: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 1 MPI thread 80: Using 2 OpenMP threads 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'spc2' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.005 0.003 195.5 80: (ns/day) (hour/ns) 80: Performance: 524.440 0.046 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 80: 80: [ OK ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 (52 ms) 80: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (53 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 94 tests from 4 test suites ran. (28697 ms total) 80: [ PASSED ] 94 tests. 80/81 Test #80: MdrunSimulatorComparison ....................... Passed 28.76 sec test 81 Start 81: MdrunVirtualSiteTests 81: Test command: /build/reproducible-path/gromacs-2022.5/build/basic-dp/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/basic-dp/Testing/Temporary/MdrunVirtualSiteTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 37 tests from 2 test suites. 81: [----------] Global test environment set-up. 81: [----------] 1 test from VirtualSiteVelocityTest 81: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 81: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 81: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 81: 81: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 2.2%. 81: The balanceable part of the MD step is 46%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 1.0%. 81: 81: 81: NOTE: 45 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.026 0.013 198.0 81: (ns/day) (hour/ns) 81: Performance: 60.339 0.398 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: trr version: GMX_trn_file (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (140 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 4.5%. 81: The balanceable part of the MD step is 49%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.2%. 81: 81: 81: NOTE: 86 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.033 0.018 181.8 81: (ns/day) (hour/ns) 81: Performance: 42.666 0.563 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (100 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 189.8 81: (ns/day) (hour/ns) 81: Performance: 333.622 0.072 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (91 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 27 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 188.2 81: (ns/day) (hour/ns) 81: Performance: 340.875 0.070 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (96 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.030 0.015 198.2 81: (ns/day) (hour/ns) 81: Performance: 51.642 0.465 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (82 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 5 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 29 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 189.2 81: (ns/day) (hour/ns) 81: Performance: 332.313 0.072 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (69 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 5 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.037 0.019 198.6 81: (ns/day) (hour/ns) 81: Performance: 41.745 0.575 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (83 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 5 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.029 0.015 198.4 81: (ns/day) (hour/ns) 81: Performance: 52.830 0.454 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (79 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 1.3%. 81: The balanceable part of the MD step is 50%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 0.6%. 81: 81: 81: NOTE: 44 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.022 0.011 197.7 81: (ns/day) (hour/ns) 81: Performance: 70.553 0.340 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (83 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.028 0.014 198.6 81: (ns/day) (hour/ns) 81: Performance: 54.931 0.437 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (71 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.029 0.015 198.5 81: (ns/day) (hour/ns) 81: Performance: 53.492 0.449 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (73 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 75 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.031 0.029 105.2 81: (ns/day) (hour/ns) 81: Performance: 26.422 0.908 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (84 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 76 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.031 0.029 104.8 81: (ns/day) (hour/ns) 81: Performance: 26.572 0.903 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (88 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 76 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.031 0.017 176.3 81: (ns/day) (hour/ns) 81: Performance: 44.858 0.535 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (79 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 76 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.030 0.029 104.3 81: (ns/day) (hour/ns) 81: Performance: 26.713 0.898 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (84 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 75 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.031 0.029 104.6 81: (ns/day) (hour/ns) 81: Performance: 26.648 0.901 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (95 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.029 0.014 198.7 81: (ns/day) (hour/ns) 81: Performance: 53.697 0.447 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (83 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 191.0 81: (ns/day) (hour/ns) 81: Performance: 357.111 0.067 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (67 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 81: 81: Using 2 MPI threads 81: Using 1 OpenMP thread per tMPI thread 81: 81: 81: NOTE: The number of threads is not equal to the number of (logical) cpus 81: and the -pin option is set to auto: will not pin threads to cpus. 81: This can lead to significant performance degradation. 81: Consider using -pin on (and -pinoffset in case you run multiple jobs). 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: NOTE: 85 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.051 0.034 151.8 81: (ns/day) (hour/ns) 81: Performance: 23.113 1.038 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022.5-Debian_2022.5_2 (double precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (84 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 81: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (1641 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 37 tests from 2 test suites ran. (1817 ms total) 81: [ PASSED ] 37 tests. 81/81 Test #81: MdrunVirtualSiteTests .......................... Passed 1.87 sec 100% tests passed, 0 tests failed out of 81 Label Time Summary: GTest = 265.00 sec*proc (79 tests) IntegrationTest = 107.05 sec*proc (23 tests) MpiTest = 148.02 sec*proc (19 tests) QuickGpuTest = 21.28 sec*proc (15 tests) SlowTest = 146.05 sec*proc (13 tests) UnitTest = 11.90 sec*proc (43 tests) Total Test time (real) = 265.90 sec touch build-basic dh_testdir /usr/bin/make -j15 -C build/mpi make[1]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/cmake -S/build/reproducible-path/gromacs-2022.5 -B/build/reproducible-path/gromacs-2022.5/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2022.5/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2022.5/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/selection /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs 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src/gromacs/selection/CMakeFiles/scanner.dir/build cd /build/reproducible-path/gromacs-2022.5 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2022.5-Debian_2022.5_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2022.5 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2022.5/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2022.5/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2022.5-2 -P /build/reproducible-path/gromacs-2022.5/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o 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'/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g 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-I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/matrix.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o -MF CMakeFiles/view_objlib.dir/view/view.cpp.o.d -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/view/view.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/bwlzh.c make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/gmx.cpp [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o -MF CMakeFiles/linearalgebra.dir/nrjac.cpp.o.d -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/nrjac.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 2%] Built target thread_mpi cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/dict.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 2%] Built target view_objlib cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/huffman.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF 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CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 2%] Built target gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 2%] Built target lmfit_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 2%] Built target mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 2%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 4%] Built target linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 6%] Built target tng_io_obj /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd 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-MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2022.5/build/mpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2022.5/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/datafilefinder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/directoryenumerator.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/exceptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/futil.cpp In file included from /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/binaryinformation.cpp:74: /build/reproducible-path/gromacs-2022.5/build/mpi/src/include/buildinfo.h:73: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.8.0" | In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/binaryinformation.cpp:60: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.9.0" | cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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-MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/cmdlineinit.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/cmdlinemodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/pargs.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/viewit.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/box.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/cellsizes.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_constraints.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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-I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/do_fit.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/veccompare.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/vecdump.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/awh_history.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include 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src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/forcebuffers.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/threaded_force_buffer.cpp cd 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src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/pbc_simd.cpp cd 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/manager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/restraintmdmodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/cubicsplinetable.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/forcetable.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/quadraticsplinetable.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/forcefieldparameters.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/topology.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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CMakeFiles/libgromacs.dir/pulling/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pullutil.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/transformationcoordinate.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/simd/support.cpp.o -MF CMakeFiles/libgromacs.dir/simd/support.cpp.o.d -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/support.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/dens_filter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_dipoles.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_make_edi.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_nmens.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/genconf.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/genion.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/grompp.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/nm2type.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/pgutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/readpull.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/autocorr.cpp cd 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/modules/displacement.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setatoms.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/runnercommon.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/topologyinformation.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/check.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/mk_angndx.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/broadcaststructs.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/calcmu.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/calcvir.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/checkpointhandler.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/compute_io.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/expanded_internal.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/electricfield.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/histogramsize.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/pointstate.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/read_params.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfitting.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/bonded.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/gpu_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/gpu_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/gpu_3dfft.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/gpu_3dfft.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/gpu_utils.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/device_management_common.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/printhardware.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -MF CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/enxio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/espio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/filetypes.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/gmx_internal_xdr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/groio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/mtxio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/position.cpp In file included from /usr/include/c++/12/vector:64, from /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.h:40, from /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:39: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = float; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateKineticEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateKineticEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = float; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/scanner_internal.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = float; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = float; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = float; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31, inlined from 'int do_cpte_nmatrix(XDR*, Enum, int, int, real**, FILE*) [with Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:1002:55: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int do_cpte_nmatrix(XDR*, Enum, int, int, real**, FILE*) [with Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = float; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullGroupEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullGroupEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = float; _Alloc = gmx::Allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = gmx::Allocator; Enum = StateEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = gmx::Allocator; Enum = StateEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = float; _Alloc = gmx::Allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selection.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEnergyEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEnergyEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateKineticEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateKineticEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include 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CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectioncollection.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectionoptionmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selelem.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selhelp.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selmethod.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selvalue.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_distance.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include 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-MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs && /usr/bin/mpicxx 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../../lib/libgromacs_mpi.so.7.0.0 ../../lib/libgromacs_mpi.so.7 ../../lib/libgromacs_mpi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 95%] Built target libgromacs /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd 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Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include 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CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include 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CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o -o ../../bin/gmx_mpi ../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/calculator.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 97%] Built target gmx cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi-dp /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2022.5/build/mpi-dp /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs /build/reproducible-path/gromacs-2022.5/build/mpi-dp /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs /build/reproducible-path/gromacs-2022.5/build/mpi-dp 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-I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers 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make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/parser.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++17 -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/scanner.cpp /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o -MF CMakeFiles/linearalgebra.dir/nrjac.cpp.o.d -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/nrjac.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers 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-I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++17 -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/tmpi_malloc.cpp /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/mdrun.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/bwlzh.c make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++17 -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/lmfit/lmmin.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o -MF CMakeFiles/view_objlib.dir/view/view.cpp.o.d -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/view/view.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/gmx.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 0%] Built target release-version-info cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/merge_sort.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 2%] Built target thread_mpi cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/vals16.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 2%] Built target view_objlib cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/warnmalloc.c cd 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-DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2022.5/src/external/tng_io/src/lib/md5.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 2%] Built target gmx_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 2%] Built target lmfit_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 2%] Built target mdrun_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 2%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 4%] Built target linearalgebra make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 6%] Built target tng_io_obj /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2022.5/build/mpi-dp /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -MF CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o.d -o CMakeFiles/modularsimulator.dir/referencetemperaturemanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/referencetemperaturemanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include 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-fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o -MF CMakeFiles/modularsimulator.dir/signallers.cpp.o.d -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/signallers.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include 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CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem 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/usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include 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-fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 8%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2022.5/build/mpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2022.5/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi-dp /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/compare.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/exceptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/filestream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/filestream.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/futil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/futil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/futil.cpp In file included from /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/binaryinformation.cpp:74: /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include/buildinfo.h:73: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.8.0" | In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/binaryinformation.cpp:60: /usr/include/x86_64-linux-gnu/hwloc/autogen/config.h:15: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.9.0" | cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/gmxassert.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -MF CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/gmxomp.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/init.cpp.o -MF CMakeFiles/libgromacs.dir/utility/init.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/init.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/keyvaluetree.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include 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src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/logger.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/message_string_collector.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/stringutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/freeenergydispatch.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/gridset.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_constraints.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/veccompare.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/vecdump.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/awh_history.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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-I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/com.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/pbcmethods.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/manager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/forcetable.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/taskassignment.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/timing/walltime_accounting.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullcoordexpressionparser.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/simd/support.cpp.o -MF CMakeFiles/libgromacs.dir/simd/support.cpp.o.d -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/support.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/anadih.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_bundle.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_disre.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_do_dssp.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_hydorder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_lie.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_mdmat.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_potential.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_rotmat.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_sans.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_saxs.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_spol.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/nrama.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gmxcpp.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include 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-std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/pdb2gmx.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/pdb2top.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/toppush.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/toputil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/vsite_parm.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/xlate.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/autocorr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/analysisdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/arraydata.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/datastorage.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/modules/average.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/modules/displacement.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/modules/frameaverager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/modules/histogram.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/modules/lifetime.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/modules/plot.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/coordinatefile.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/outputselector.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/analysismodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/msd.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/pairdist.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/runnercommon.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/topologyinformation.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/check.cpp.o -MF CMakeFiles/libgromacs.dir/tools/check.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/check.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/mk_angndx.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/report_methods.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/trjconv.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/broadcaststructs.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/calc_verletbuf.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/md_support.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/perf_est.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/stat.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/update_vv.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/coordstate.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/correlationgrid.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/correlationhistory.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfitting.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/orires.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/ewald_utils.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 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/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include 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CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/fft.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/fft5d.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/parallel_3dfft.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/gpu_3dfft.cpp.o 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/fft_fftw3.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && 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-std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include 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-std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/abstractoption.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -MF CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -MF CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include 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-std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/options.cpp.o -MF CMakeFiles/libgromacs.dir/options/options.cpp.o.d -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsection.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -MF CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o.d -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/confio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/enxio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/espio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/gmx_internal_xdr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/matio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/mtxio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/readinp.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/timecontrol.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/warninp.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/writeps.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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-MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/poscalc.cpp In file included from /usr/include/c++/12/vector:64, from /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.h:40, from /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:39: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullGroupEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullGroupEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/position.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/scanner_internal.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31, inlined from 'int do_cpte_nmatrix(XDR*, Enum, int, int, real**, FILE*) [with Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:1002:55: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selection.cpp /usr/include/c++/12/bits/vector.tcc: In function 'int do_cpte_nmatrix(XDR*, Enum, int, int, real**, FILE*) [with Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = gmx::Allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = gmx::Allocator; Enum = StateEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = gmx::Allocator; Enum = StateEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = double; _Alloc = gmx::Allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEnergyEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEnergyEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateKineticEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateKineticEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectioncollection.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]', inlined from 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateFepEntry]' at /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: /usr/include/c++/12/bits/stl_vector.h:1011:28: warning: 'this' pointer is null [-Wnonnull] 1011 | _M_default_append(__new_size - size()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateFepEntry]': /usr/include/c++/12/bits/vector.tcc:626:5: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::_M_default_append(size_type) [with _Tp = int; _Alloc = std::allocator]' 626 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectionoption.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectionoptionmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selelem.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selhelp.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selmethod.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selvalue.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_distance.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_insolidangle.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_position.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so -lm /usr/lib/x86_64-linux-gnu/libmuparser.so.2.3.3 /usr/lib/x86_64-linux-gnu/liblapack.so -lm /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_mpi_d.so.7.0.0 ../../lib/libgromacs_mpi_d.so.7 ../../lib/libgromacs_mpi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs /build/reproducible-path/gromacs-2022.5/build/mpi-dp /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib /build/reproducible-path/gromacs-2022.5/build/mpi-dp /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include 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CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o -o ../../bin/gmx_mpi_d ../../lib/libgromacs_mpi_d.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include 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/build/reproducible-path/gromacs-2022.5/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/calculator.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [ 97%] Built target gmx cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include 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/build/reproducible-path/gromacs-2022.5/build/mpi-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi-dp' cd /build/reproducible-path/gromacs-2022.5/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/samples /build/reproducible-path/gromacs-2022.5/build/mpi-dp 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/build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs 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CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build cd /build/reproducible-path/gromacs-2022.5 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2022.5-Debian_2022.5_2 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2022.5 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2022.5/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2022.5/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2022.5-2 -P /build/reproducible-path/gromacs-2022.5/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/build [ 0%] Built target scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/external/googletest/googletest && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++17 -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/src/gtest-all.cc /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 0%] Built target mdrun_objlib /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 0%] Built target release-version-info make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 1%] Built target thread_mpi /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build [ 1%] Built target lmfit_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 2%] Built target tng_io_obj /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color= [ 4%] Built target linearalgebra make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 5%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 62%] Built target libgromacs /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 63%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/samples /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake --color= /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/samples /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 63%] Built target methane-water-integration [ 63%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.11.0 -o ../../../../lib/libgtest.so.1.11.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 63%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/external/googletest/googlemock /build/reproducible-path/gromacs-2022.5/build/mpi/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/external/googletest/googlemock && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -I/build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++17 -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so.1.11.0 -o ../../../../lib/libgmock.so.1.11.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 63%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/trajectoryreader.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 64%] Built target testutils /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/build.make api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend make[4]: 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-I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/alignedallocator.cpp.o -MF CMakeFiles/utility-test.dir/alignedallocator.cpp.o.d -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/alignedallocator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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-I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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-DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 64%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/simulatorcomparison.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mpi.so.7.0.0 ../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/terminationhelper.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 64%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem 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CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests/bias.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 64%] Built target applied_forces-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasgrid.cpp.o -MF CMakeFiles/awh-test.dir/biasgrid.cpp.o.d -o CMakeFiles/awh-test.dir/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests/biasgrid.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 64%] Built target testutils-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f 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/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 66%] Built target nbnxm-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests/biassharing.cpp /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 66%] Built target nblib_test_infrastructure /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biasstate.cpp.o -MF CMakeFiles/awh-test.dir/biasstate.cpp.o.d -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/tests/biasstate.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 67%] Built target domdec-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/fft/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fft/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/tests/pairs.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fft/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include 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/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd 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cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 67%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include 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-Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include 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-fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/device_availability.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -MF CMakeFiles/ewald-test.dir/pmegathertest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src 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"CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src 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src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external 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directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 68%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make 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/build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/ebin.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 68%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/tests/extents.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fft/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem 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&& /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -MF CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask128.cpp.o -MF CMakeFiles/utility-test.dir/bitmask128.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/bitmask128.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 68%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests/helpformat.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 70%] Built target fft-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoption.cpp.o -MF CMakeFiles/options-test.dir/filenameoption.cpp.o.d -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/filenameoption.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/coordinatetransformation.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/tests/mockhardwaretopology.cpp [ 70%] Built target listed_forces-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/cstringutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. 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-DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/tests/device_management.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 72%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -MF CMakeFiles/random-test.dir/exponentialdistribution.cpp.o.d -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem 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CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF 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-I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/repeatingsection.cpp.o -MF CMakeFiles/options-test.dir/repeatingsection.cpp.o.d -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" 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-I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o 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Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-MF CMakeFiles/restraintpotential-test.dir/manager.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/tests/manager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem 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CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF 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'/build/reproducible-path/gromacs-2022.5/build/mpi' [ 74%] Built target mdspan-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 75%] Built target pbcutil-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tables/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tables/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 77%] Built target mdtypes-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/threefry.cpp.o -MF CMakeFiles/random-test.dir/threefry.cpp.o.d -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/threefry.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/random/tests/uniformintdistribution.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 77%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/timing/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/timing/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/timing/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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"CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/logger.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 77%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/settletestrunners.cpp [ 77%] Built target timing-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pme.cpp.o -MF CMakeFiles/ewald-test.dir/pme.cpp.o.d -o CMakeFiles/ewald-test.dir/pme.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/tests/pme.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pulling/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/treesupport.cpp.o -MF CMakeFiles/options-test.dir/treesupport.cpp.o.d -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/tests/treesupport.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 77%] Built target taskassignment-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/utility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/utility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/message_string_collector.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 77%] Built target random-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/compat/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/compat/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem 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src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/compat/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/compat/tests/mp11.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/path.cpp.o -MF CMakeFiles/utility-test.dir/path.cpp.o.d -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/path.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -MF CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o.d -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/physicalnodecommunicator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 77%] Built target ewald-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/compat/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/compat/tests/pointers.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pulling/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lmuparser -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/mtop.cpp.o -MF CMakeFiles/topology-test.dir/mtop.cpp.o.d -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests/mtop.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/scalar.cpp [ 77%] Built target pull-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/editconf.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tables/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/compat/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT 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/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -MF CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o.d -o CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/tests/wholemoleculetransform.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 77%] Built target table-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 77%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 77%] Built target options-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. 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-I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 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-I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF 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/build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/multidimarray.cpp.o -MF CMakeFiles/math-test.dir/multidimarray.cpp.o.d -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/multidimarray.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textwriter.cpp.o -MF CMakeFiles/utility-test.dir/textwriter.cpp.o.d -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/tests/textwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock 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"CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/tests/correlationdataset.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 78%] Built target mdlib-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF 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/build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/symtab.cpp.o -MF CMakeFiles/topology-test.dir/symtab.cpp.o.d -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests/symtab.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests && 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/scalar_math.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 78%] Built target gmxana-test /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/builder.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include 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-fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -MF CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o.d -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/paddedvector.cpp.o -MF CMakeFiles/math-test.dir/paddedvector.cpp.o.d -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/tests/paddedvector.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 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-I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 78%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -MF CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/dump.cpp.o -MF CMakeFiles/tool-test.dir/dump.cpp.o.d -o CMakeFiles/tool-test.dir/dump.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests/dump.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -MF CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o.d -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/outputadapters.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp [ 78%] Built target pdb2gmx3-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/requirements.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/helpwriting.cpp.o -MF CMakeFiles/tool-test.dir/helpwriting.cpp.o.d -o CMakeFiles/tool-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests/helpwriting.cpp [ 79%] Built target correlations-test /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/indexutil.cpp.o -MF CMakeFiles/selection-test.dir/indexutil.cpp.o.d -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/indexutil.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 79%] Built target pdb2gmx2-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/compressed_x_output.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 79%] Built target energyanalysis-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock 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-DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/setatoms.cpp [ 81%] Built target utility-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/tests/convert-tpr.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 82%] Built target topology-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/multiple_time_stepping.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. 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-I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/readir.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 82%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/ewaldsurfaceterm.cpp /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 82%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/minimize.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/nonbonded_bench.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 82%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/tpitest.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/freezegroups.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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/build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 82%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 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CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/domain_decomposition.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/rerun.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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'/build/reproducible-path/gromacs-2022.5/build/mpi' [ 82%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake --color= /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/multisim.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/readinp.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 83%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 85%] Built target gmxpreprocess-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/grompp.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 85%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem 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"CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/tests/tngio.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 86%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem 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/usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem 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-Wl,-z,now "CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 86%] Built target mdrun-multisim-test /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/periodicactions_basic.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp [ 86%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/DependInfo.cmake --color= [ 86%] Built target mdrun-non-integrator-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/periodicactions.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 86%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 87%] Built target math-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp [ 87%] Built target mdrun-mpi-pme-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests/periodicactions_constraints.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 87%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-coupling-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 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89%] Built target mdrun-mpi-coordination-coupling-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 ../../../../lib/libgmock.so.1.11.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.11.0 In file included from /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include/gtest/gtest.h:60, from /build/reproducible-path/gromacs-2022.5/api/nblib/tests/tpr.cpp:43: /build/reproducible-path/gromacs-2022.5/api/nblib/tests/tpr.cpp: In member function 'virtual void nblib::test::TprReaderTest_Spc2Reads_Test::TestBody()': /build/reproducible-path/gromacs-2022.5/api/nblib/tests/tpr.cpp:91:48: warning: ignoring return value of 'std::vector<_Tp, _Alloc>::size_type std::vector<_Tp, _Alloc>::size() const [with _Tp = gmx::BasicVector; _Alloc = std::allocator >; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 91 | EXPECT_NO_THROW(tprReader.coordinates_.size()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/12/vector:64, from /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include/gtest/gtest.h:58: /usr/include/c++/12/bits/stl_vector.h:987:7: note: declared here 987 | size() const _GLIBCXX_NOEXCEPT | ^~~~ cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 89%] Built target selection-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend [ 90%] Built target mdrun-fep-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2022.5/build/mpi 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-I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/bondtypes.cpp /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/util/tests/setup.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-mpi-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-mpi-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-mpi-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/simstate.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 91%] Built target mdrun-mpi-coordination-constraints-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make 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/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem 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'/build/reproducible-path/gromacs-2022.5/build/mpi' [ 91%] Built target mdrun-mpi-coordination-basic-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o 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/build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/gmxcalculator.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 91%] Built target mdrun-vsites-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= [ 93%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -MF CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/nbnxmsetup.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 ../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 ../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/moduletest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 93%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 93%] Built target nblib-tpr-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/arraydata.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 93%] Built target mdrun-simulator-comparison-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 ../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 94%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 94%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/helpers.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 95%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 95%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/tests/average.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 95%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/tests/filenm.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/topology.cpp.o -MF CMakeFiles/nblib-setup-test.dir/topology.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/tests/topology.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops 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src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 97%] Built target commandline-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o -c /build/reproducible-path/gromacs-2022.5/api/nblib/listed_forces/tests/transformations.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/api -I/build/reproducible-path/gromacs-2022.5/src/testutils/include -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -msse4.1 -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++17 -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 In member function 'virtual void {anonymous}::UnionFinderTest_WorksEmpty_Test::TestBody()': cc1plus: warning: iteration 2147483648 invokes undefined behavior [-Waggressive-loop-optimizations] In file included from /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/unionfind.cpp:43: In member function 'std::vector gmx::UnionFinder::allSizes()', inlined from 'virtual void {anonymous}::UnionFinderTest_WorksEmpty_Test::TestBody()' at /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/unionfind.cpp:60:5: /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/unionfind.h:118:27: note: within this loop 118 | for (int i = 0; i < count; ++i) | ~~^~~~~~~ make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 97%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [ 98%] Built target trajectoryanalysis-test cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.11.0 ../../../lib/libgtest.so.1.11.0 ../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [100%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/api/nblib /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [100%] Built target nblib-tests cd /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.11.0 ../../../../lib/libgtest.so.1.11.0 ../../../../lib/libgromacs_mpi.so.7.0.0 -lm /usr/lib/gcc/x86_64-linux-gnu/12/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [100%] Built target nblib-listed-forces-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' cd /build/reproducible-path/gromacs-2022.5/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi /build/reproducible-path/gromacs-2022.5/build/mpi/CMakeFiles/tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2022.5/build/mpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' make[1]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/mpi' (cd build/mpi ; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2022.5/build/mpi/lib \ OMPI_MCA_plm_rsh_agent=/bin/false \ OMPI_MCA_rmaps_base_oversubscribe=1 \ ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2022.5/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2022.5/build/mpi/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2022.5/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2022.5/build/mpi/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2022.5/build/mpi Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: NbLibListedForcesTests 1: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/NbLibListedForcesTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/listed_forces/tests 1: Test timeout computed to be: 600 1: [==========] Running 44 tests from 22 test suites. 1: [----------] Global test environment set-up. 1: [----------] 8 tests from NBlibTest 1: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 1: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 1: [ RUN ] NBlibTest.BondTypesLessThanWorks 1: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 1: [ RUN ] NBlibTest.CanSplitListedWork 1: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 1: [ RUN ] NBlibTest.ListedForceBuffer 1: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 1: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 1: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 1: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 1: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 1: [ RUN ] NBlibTest.EndToEndListedComparison 1: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 1: [ RUN ] NBlibTest.shiftForcesAreCorrect 1: [ OK ] NBlibTest.shiftForcesAreCorrect (30 ms) 1: [----------] 8 tests from NBlibTest (31 ms total) 1: 1: [----------] 1 test from Kernels 1: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 1: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 1: [----------] 1 test from Kernels (0 ms total) 1: 1: [----------] 1 test from FourCenter 1: [ RUN ] FourCenter.ListedForcesProperDihedralTest 1: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 1: [----------] 1 test from FourCenter (0 ms total) 1: 1: [----------] 7 tests from ThreeCenter 1: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 1: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 1: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 1: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 1: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 1: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 1: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 1: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 1: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 1: [----------] 7 tests from ThreeCenter (0 ms total) 1: 1: [----------] 5 tests from TwoCenter 1: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 1: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 1: [ RUN ] TwoCenter.ListedForcesG96BondTest 1: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 1: [ RUN ] TwoCenter.ListedForcesCubicBondTest 1: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 1: [ RUN ] TwoCenter.ListedForcesMorseBondTest 1: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 1: [ RUN ] TwoCenter.ListedForcesFeneBondTest 1: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 1: [----------] 5 tests from TwoCenter (0 ms total) 1: 1: [----------] 5 tests from ListedExampleData 1: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 1: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 1: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 1: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 1: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 1: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 1: [ RUN ] ListedExampleData.CanReduceForces 1: [ OK ] ListedExampleData.CanReduceForces (0 ms) 1: [ RUN ] ListedExampleData.CanReduceEnergies 1: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 1: [----------] 5 tests from ListedExampleData (0 ms total) 1: 1: [----------] 1 test from LinearChainDataFixture 1: [ RUN ] LinearChainDataFixture.Multithreading 1: [ OK ] LinearChainDataFixture.Multithreading (3 ms) 1: [----------] 1 test from LinearChainDataFixture (3 ms total) 1: 1: [----------] 2 tests from ListedShims 1: [ RUN ] ListedShims.ParameterConversion 1: [ OK ] ListedShims.ParameterConversion (0 ms) 1: [ RUN ] ListedShims.GmxToNblibConversion 1: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 1: [----------] 2 tests from ListedShims (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 1: 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 1: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 1: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 1: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 1: 1: [----------] 1 test from ListedTransformations 1: [ RUN ] ListedTransformations.SortInteractionIndices 1: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 1: [----------] 1 test from ListedTransformations (0 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 44 tests from 22 test suites ran. (37 ms total) 1: [ PASSED ] 44 tests. 1/81 Test #1: NbLibListedForcesTests ......................... Passed 1.09 sec test 2 Start 2: NbLibSamplesTestArgon 2: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/argon-forces-integration 2: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/samples 2: Test timeout computed to be: 1500 2: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 2: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 2: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 2: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 2/81 Test #2: NbLibSamplesTestArgon .......................... Passed 0.02 sec test 3 Start 3: NbLibSamplesTestMethaneWater 3: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/methane-water-integration 3: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/samples 3: Test timeout computed to be: 1500 3: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 3: final position of particle 9: x 77.358398 y 5.324913 z -80.600098 3/81 Test #3: NbLibSamplesTestMethaneWater ................... Passed 0.02 sec test 4 Start 4: NbLibUtilTests 4: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/NbLibUtilTests.xml" 4: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/util/tests 4: Test timeout computed to be: 30 4: [==========] Running 16 tests from 2 test suites. 4: [----------] Global test environment set-up. 4: [----------] 6 tests from NBlibTest 4: [ RUN ] NBlibTest.isRealValued 4: [ OK ] NBlibTest.isRealValued (0 ms) 4: [ RUN ] NBlibTest.checkNumericValuesHasNan 4: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 4: [ RUN ] NBlibTest.checkNumericValuesHasInf 4: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 4: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 4: Velocities were taken from a Maxwell distribution at 300 K 4: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 4: [ RUN ] NBlibTest.generateVelocitySize 4: Velocities were taken from a Maxwell distribution at 300 K 4: [ OK ] NBlibTest.generateVelocitySize (0 ms) 4: [ RUN ] NBlibTest.generateVelocityCheckNumbers 4: Velocities were taken from a Maxwell distribution at 300 K 4: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 4: [----------] 6 tests from NBlibTest (0 ms total) 4: 4: [----------] 10 tests from NblibTraitsUtils 4: [ RUN ] NblibTraitsUtils.FuseTwo 4: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 4: [ RUN ] NblibTraitsUtils.Fuse 4: [ OK ] NblibTraitsUtils.Fuse (0 ms) 4: [ RUN ] NblibTraitsUtils.Repeat 4: [ OK ] NblibTraitsUtils.Repeat (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTuple1 4: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTuple2 4: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 4: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 4: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 4: [ RUN ] NblibTraitsUtils.Contains 4: [ OK ] NblibTraitsUtils.Contains (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 4: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 4: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 4: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 4: [----------] 10 tests from NblibTraitsUtils (0 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 16 tests from 2 test suites ran. (0 ms total) 4: [ PASSED ] 16 tests. 4/81 Test #4: NbLibUtilTests ................................. Passed 0.52 sec test 5 Start 5: NbLibSetupTests 5: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/NbLibSetupTests.xml" 5: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests 5: Test timeout computed to be: 600 5: [==========] Running 56 tests from 3 test suites. 5: [----------] Global test environment set-up. 5: [----------] 41 tests from NBlibTest 5: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 5: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 5: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 5: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 5: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 5: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 5: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 5: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 5: [ RUN ] NBlibTest.CubicBoxWorks 5: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 5: [ RUN ] NBlibTest.BoxEqual 5: [ OK ] NBlibTest.BoxEqual (0 ms) 5: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 5: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 5: [ RUN ] NBlibTest.CanMergeInteractions 5: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 5: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 5: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 5: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 5: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 5: [ RUN ] NBlibTest.PbcHolderWorks 5: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 5: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 5: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 5: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 5: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 5: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 5: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 5: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 5: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 5: [ RUN ] NBlibTest.AtWorks 5: [ OK ] NBlibTest.AtWorks (0 ms) 5: [ RUN ] NBlibTest.AtThrows 5: [ OK ] NBlibTest.AtThrows (0 ms) 5: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 5: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 5: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 5: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 5: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 5: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 5: [ RUN ] NBlibTest.CanAddInteractions 5: [ OK ] NBlibTest.CanAddInteractions (0 ms) 5: [ RUN ] NBlibTest.CanAddUreyBradley 5: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 5: [ RUN ] NBlibTest.TopologyHasNumParticles 5: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 5: [ RUN ] NBlibTest.TopologyHasCharges 5: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 5: [ RUN ] NBlibTest.TopologyHasMasses 5: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 5: [ RUN ] NBlibTest.TopologyHasParticleTypes 5: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 5: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 5: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 5: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 5: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 5: [ RUN ] NBlibTest.TopologyHasExclusions 5: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 5: [ RUN ] NBlibTest.TopologyHasSequencing 5: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 5: [ RUN ] NBlibTest.TopologyCanAggregateBonds 5: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 5: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 5: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 5: [ RUN ] NBlibTest.TopologySequenceIdThrows 5: No particle O-Atom in residue SOL in molecule SOL found 5: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 5: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 5: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 5: [ RUN ] NBlibTest.TopologyListedInteractions 5: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 5: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 5: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 5: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 5: No particle Iron in residue SOL in molecule SOL found 5: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 5: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 5: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 5: [----------] 41 tests from NBlibTest (3 ms total) 5: 5: [----------] 14 tests from NbnxmSetupTest 5: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 5: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 5: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 5: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 5: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 5: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 5: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 5: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 5: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 5: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 5: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 5: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 5: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 5: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 5: [ RUN ] NbnxmSetupTest.updateForcerecWorks 5: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 5: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 5: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 5: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 5: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 5: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 5: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 5: [----------] 14 tests from NbnxmSetupTest (0 ms total) 5: 5: [----------] 1 test from VirialsTest 5: [ RUN ] VirialsTest.computeVirialTensorWorks 5: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 5: [----------] 1 test from VirialsTest (0 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 56 tests from 3 test suites ran. (4 ms total) 5: [ PASSED ] 56 tests. 5/81 Test #5: NbLibSetupTests ................................ Passed 0.60 sec test 6 Start 6: NbLibTprTests 6: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/NbLibTprTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests 6: Test timeout computed to be: 30 6: [==========] Running 4 tests from 1 test suite. 6: [----------] Global test environment set-up. 6: [----------] 4 tests from TprReaderTest 6: [ RUN ] TprReaderTest.SimDBTprIsCreated 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Number of degrees of freedom in T-Coupling group System is 33.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 6: NVE simulation: will use the initial temperature of 68.810 K for 6: determining the Verlet buffer size 6: 6: 6: There were 3 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 6: Generated 1 of the 1 non-bonded parameter combinations 6: 6: Excluding 1 bonded neighbours molecule type 'Argon' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.SimDBTprIsCreated (39 ms) 6: [ RUN ] TprReaderTest.Spc2Reads 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Generating 1-4 interactions: fudge = 0.5 6: Number of degrees of freedom in T-Coupling group System is 9.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: NVE simulation: will use the initial temperature of 2573.591 K for 6: determining the Verlet buffer size 6: 6: 6: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 6: You are using a plain Coulomb cut-off, which might produce artifacts. 6: You might want to consider using PME electrostatics. 6: 6: 6: 6: There were 4 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 6: Generated 3 of the 3 non-bonded parameter combinations 6: 6: Generated 3 of the 3 1-4 parameter combinations 6: 6: Excluding 2 bonded neighbours molecule type 'SOL' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.Spc2Reads (23 ms) 6: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Number of degrees of freedom in T-Coupling group System is 33.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 6: NVE simulation: will use the initial temperature of 68.810 K for 6: determining the Verlet buffer size 6: 6: 6: There were 3 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 6: Generated 1 of the 1 non-bonded parameter combinations 6: 6: Excluding 1 bonded neighbours molecule type 'Argon' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (32 ms) 6: [ RUN ] TprReaderTest.FCfromTprDataWorks 6: 6: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 6: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 6: that with the Verlet scheme, nstlist has no effect on the accuracy of 6: your simulation. 6: 6: 6: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 6: Setting nstcalcenergy (100) equal to nstenergy (4) 6: 6: Number of degrees of freedom in T-Coupling group System is 33.00 6: 6: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 6: NVE simulation: will use the initial temperature of 68.810 K for 6: determining the Verlet buffer size 6: 6: 6: There were 3 notes 6: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 6: Generated 1 of the 1 non-bonded parameter combinations 6: 6: Excluding 1 bonded neighbours molecule type 'Argon' 6: 6: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 6: 6: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 6: 6: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 6: 6: Note that mdrun will redetermine rlist based on the actual pair-list setup 6: 6: This run will generate roughly 0 Mb of data 6: [ OK ] TprReaderTest.FCfromTprDataWorks (31 ms) 6: [----------] 4 tests from TprReaderTest (128 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 4 tests from 1 test suite ran. (173 ms total) 6: [ PASSED ] 4 tests. 6/81 Test #6: NbLibTprTests .................................. Passed 0.70 sec test 7 Start 7: NbLibIntegrationTests 7: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/NbLibIntegrationTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 20 tests from 1 test suite. 7: [----------] Global test environment set-up. 7: [----------] 20 tests from NBlibTest 7: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 7: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 7: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 7: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 7: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 7: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 7: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 7: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 7: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 7: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 7: [ RUN ] NBlibTest.ExpectedNumberOfForces 7: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 7: [ RUN ] NBlibTest.CanIntegrateSystem 7: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 7: [ RUN ] NBlibTest.UpdateChangesForces 7: [ OK ] NBlibTest.UpdateChangesForces (1 ms) 7: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 7: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 7: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 7: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 7: [ RUN ] NBlibTest.CanConstructSimulationState 7: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 7: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 7: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 7: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 7: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 7: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 7: [ RUN ] NBlibTest.SimulationStateCanMove 7: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 7: [ RUN ] NBlibTest.SimulationStateCanAssign 7: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 7: [ RUN ] NBlibTest.SimulationStateHasBox 7: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 7: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 7: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 7: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 7: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 7: [----------] 20 tests from NBlibTest (7 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 20 tests from 1 test suite ran. (7 ms total) 7: [ PASSED ] 20 tests. 7/81 Test #7: NbLibIntegrationTests .......................... Passed 0.48 sec test 8 Start 8: NbLibIntegratorTests 8: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/NbLibIntegratorTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/api/nblib/tests 8: Test timeout computed to be: 600 8: [==========] Running 1 test from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 1 test from NBlibTest 8: [ RUN ] NBlibTest.IntegratorWorks 8: [ OK ] NBlibTest.IntegratorWorks (0 ms) 8: [----------] 1 test from NBlibTest (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 1 test from 1 test suite ran. (0 ms total) 8: [ PASSED ] 1 test. 8/81 Test #8: NbLibIntegratorTests ........................... Passed 0.57 sec test 9 Start 9: TestUtilsUnitTests 9: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/TestUtilsUnitTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils/tests 9: Test timeout computed to be: 30 9: [==========] Running 59 tests from 5 test suites. 9: [----------] Global test environment set-up. 9: [----------] 10 tests from InteractiveTestHelperTest 9: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 9: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 9: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 9: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 9: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 9: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 9: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 9: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 9: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 9: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 9: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 9: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 9: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 9: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 9: [----------] 10 tests from InteractiveTestHelperTest (3 ms total) 9: 9: [----------] 34 tests from ReferenceDataTest 9: [ RUN ] ReferenceDataTest.HandlesSimpleData 9: [ OK ] ReferenceDataTest.HandlesSimpleData (3 ms) 9: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 9: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 9: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesStringBlockData 9: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesVectorData 9: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSequenceData 9: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 9: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesIncorrectData 9: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 9: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMissingData 9: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUncheckedData 9: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 9: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 9: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesAnys 9: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 9: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 9: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 9: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 9: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 9: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 9: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 9: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 9: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 9: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 9: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 9: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 9: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (5 ms) 9: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 9: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 9: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesReadingValues 9: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 9: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 9: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 9: [----------] 34 tests from ReferenceDataTest (15 ms total) 9: 9: [----------] 7 tests from FloatingPointDifferenceTest 9: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 9: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 9: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 9: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 9: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 9: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 9: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 9: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 9: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 9: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 9: 9: [----------] 4 tests from FloatingPointToleranceTest 9: [ RUN ] FloatingPointToleranceTest.UlpTolerance 9: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 9: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 9: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 9: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 9: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 9: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 9: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 9: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 9: 9: [----------] 4 tests from XvgTests 9: [ RUN ] XvgTests.CreateFile 9: [ OK ] XvgTests.CreateFile (0 ms) 9: [ RUN ] XvgTests.CheckMissing 9: [ OK ] XvgTests.CheckMissing (1 ms) 9: [ RUN ] XvgTests.CheckExtra 9: [ OK ] XvgTests.CheckExtra (0 ms) 9: [ RUN ] XvgTests.ReadIncorrect 9: [ OK ] XvgTests.ReadIncorrect (0 ms) 9: [----------] 4 tests from XvgTests (3 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 59 tests from 5 test suites ran. (22 ms total) 9: [ PASSED ] 59 tests. 9/81 Test #9: TestUtilsUnitTests ............................. Passed 0.52 sec test 10 Start 10: TestUtilsMpiUnitTests 10: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/testutils-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/TestUtilsMpiUnitTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/testutils/tests 10: Test timeout computed to be: 30 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from MpiSelfTest 10: [ RUN ] MpiSelfTest.Runs 10: [ OK ] MpiSelfTest.Runs (33 ms) 10: [----------] 1 test from MpiSelfTest (37 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (37 ms total) 10: [ PASSED ] 1 test. 10/81 Test #10: TestUtilsMpiUnitTests .......................... Passed 0.55 sec test 11 Start 11: UtilityUnitTests 11: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/UtilityUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests 11: Test timeout computed to be: 30 11: [==========] Running 386 tests from 61 test suites. 11: [----------] Global test environment set-up. 11: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/0.Move 11: [ OK ] AllocatorTest/0.Move (0 ms) 11: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/0 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/1.Move 11: [ OK ] AllocatorTest/1.Move (0 ms) 11: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/1 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/2.Move 11: [ OK ] AllocatorTest/2.Move (0 ms) 11: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/2 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/3.Move 11: [ OK ] AllocatorTest/3.Move (0 ms) 11: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/3 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 11: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/4.Move 11: [ OK ] AllocatorTest/4.Move (0 ms) 11: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/4 (0 ms total) 11: 11: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 11: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 11: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 11: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 11: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 11: [ RUN ] AllocatorTest/5.Move 11: [ OK ] AllocatorTest/5.Move (0 ms) 11: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 11: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 11: [----------] 5 tests from AllocatorTest/5 (0 ms total) 11: 11: [----------] 1 test from AllocatorUntypedTest 11: [ RUN ] AllocatorUntypedTest.Comparison 11: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 11: [----------] 1 test from AllocatorUntypedTest (0 ms total) 11: 11: [----------] 4 tests from EmptyArrayRefTest 11: [ RUN ] EmptyArrayRefTest.IsEmpty 11: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 11: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 11: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 11: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 11: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 11: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 11: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 11: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 11: 11: [----------] 1 test from EmptyConstArrayRefTest 11: [ RUN ] EmptyConstArrayRefTest.IsEmpty 11: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 11: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 11: 11: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 11: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 11: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 11: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 11: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 11: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 11: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 11: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 11: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 11: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 11: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 11: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 11: 11: [----------] 2 tests from CStringUtilityTest 11: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 11: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 11: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 11: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 11: [----------] 2 tests from CStringUtilityTest (0 ms total) 11: 11: [----------] 2 tests from DefaultInitializationAllocator 11: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 11: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 11: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 11: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 11: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 11: 11: [----------] 4 tests from EnumerationHelpersTest 11: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 11: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 11: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 11: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 11: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 11: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 11: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 11: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 11: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 11: 11: [----------] 9 tests from FixedCapacityVectorTest 11: [ RUN ] FixedCapacityVectorTest.IsEmpty 11: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 11: [ RUN ] FixedCapacityVectorTest.PushWorks 11: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.PopWorks 11: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.ClearWorks 11: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 11: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.AtThrows 11: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 11: [ RUN ] FixedCapacityVectorTest.IteratorWorks 11: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 11: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 11: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 11: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 11: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 11: 11: [----------] 5 tests from InMemorySerializerTest 11: [ RUN ] InMemorySerializerTest.Roundtrip 11: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 11: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 11: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 11: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 11: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 11: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 11: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 11: [ RUN ] InMemorySerializerTest.SizeIsCorrect 11: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 11: [----------] 5 tests from InMemorySerializerTest (0 ms total) 11: 11: [----------] 4 tests from KeyValueTreeSerializerTest 11: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 11: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 11: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 11: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 11: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 11: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms) 11: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 11: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 11: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total) 11: 11: [----------] 6 tests from TreeValueTransformTest 11: [ RUN ] TreeValueTransformTest.SimpleTransforms 11: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 11: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 11: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 11: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 11: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 11: [ RUN ] TreeValueTransformTest.ObjectFromString 11: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 11: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 11: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 11: [ RUN ] TreeValueTransformTest.ScopedTransformRules 11: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 11: [----------] 6 tests from TreeValueTransformTest (1 ms total) 11: 11: [----------] 1 test from TreeValueTransformErrorTest 11: [ RUN ] TreeValueTransformErrorTest.ConversionError 11: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 11: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 11: 11: [----------] 9 tests from ListOfLists 11: [ RUN ] ListOfLists.EmptyListOfListsWorks 11: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 11: [ RUN ] ListOfLists.AppendWorks 11: [ OK ] ListOfLists.AppendWorks (0 ms) 11: [ RUN ] ListOfLists.EmptyListWorks 11: [ OK ] ListOfLists.EmptyListWorks (0 ms) 11: [ RUN ] ListOfLists.AppendAccessWorks 11: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 11: [ RUN ] ListOfLists.ClearWorks 11: [ OK ] ListOfLists.ClearWorks (0 ms) 11: [ RUN ] ListOfLists.OutOfRangeAccessThrows 11: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 11: [ RUN ] ListOfLists.FrontAndBackWork 11: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 11: [ RUN ] ListOfLists.ExtractsAndRestores 11: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 11: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 11: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 11: [----------] 9 tests from ListOfLists (0 ms total) 11: 11: [----------] 7 tests from LoggerTest 11: [ RUN ] LoggerTest.EmptyLoggerWorks 11: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 11: [ RUN ] LoggerTest.LogsToStream 11: [ OK ] LoggerTest.LogsToStream (0 ms) 11: [ RUN ] LoggerTest.LogsToFile 11: [ OK ] LoggerTest.LogsToFile (1 ms) 11: [ RUN ] LoggerTest.LevelFilteringWorks 11: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 11: [ RUN ] LoggerTest.LogsToMultipleStreams 11: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 11: [ RUN ] LoggerTest.LogsToMultipleFiles 11: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 11: [ RUN ] LoggerTest.LogsToStreamAndFile 11: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 11: [----------] 7 tests from LoggerTest (1 ms total) 11: 11: [----------] 4 tests from MDModulesNotifierTest 11: [ RUN ] MDModulesNotifierTest.AddConsumer 11: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 11: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 11: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 11: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 11: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 11: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 11: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 11: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 11: 11: [----------] 7 tests from MessageStringCollectorTest 11: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 11: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 11: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 11: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 11: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 11: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 11: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 11: [ RUN ] MessageStringCollectorTest.CanMoveAssign 11: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 11: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 11: 11: [----------] 1 test from PathTest 11: [ RUN ] PathTest.StripSourcePrefixWorks 11: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 11: [----------] 1 test from PathTest (0 ms total) 11: 11: [----------] 2 tests from PhysicalNodeCommunicatorTest 11: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 11: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 11: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 11: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 11: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 11: 11: [----------] 5 tests from Range 11: [ RUN ] Range.EmptyRangeWorks 11: [ OK ] Range.EmptyRangeWorks (0 ms) 11: [ RUN ] Range.NonEmptyRangeWorks 11: [ OK ] Range.NonEmptyRangeWorks (0 ms) 11: [ RUN ] Range.BeginEnd 11: [ OK ] Range.BeginEnd (0 ms) 11: [ RUN ] Range.IsInRangeWorks 11: [ OK ] Range.IsInRangeWorks (0 ms) 11: [ RUN ] Range.IteratorWorks 11: [ OK ] Range.IteratorWorks (0 ms) 11: [----------] 5 tests from Range (0 ms total) 11: 11: [----------] 7 tests from StringConvert 11: [ RUN ] StringConvert.NoResultFromEptyString 11: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 11: [ RUN ] StringConvert.ThreeFloatsSuccessfully 11: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 11: [ RUN ] StringConvert.OneIntSucessfully 11: [ OK ] StringConvert.OneIntSucessfully (0 ms) 11: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 11: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 11: [ RUN ] StringConvert.ThrowsWhenWrongSize 11: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 11: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 11: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 11: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 11: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 11: [----------] 7 tests from StringConvert (0 ms total) 11: 11: [----------] 7 tests from StringToEnumValueConverterTest 11: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 11: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 11: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 11: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 11: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 11: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 11: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 11: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 11: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 11: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 11: 11: [----------] 9 tests from StringUtilityTest 11: [ RUN ] StringUtilityTest.StartsWith 11: [ OK ] StringUtilityTest.StartsWith (0 ms) 11: [ RUN ] StringUtilityTest.EndsWith 11: [ OK ] StringUtilityTest.EndsWith (0 ms) 11: [ RUN ] StringUtilityTest.StripSuffixIfPresent 11: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 11: [ RUN ] StringUtilityTest.StripString 11: [ OK ] StringUtilityTest.StripString (0 ms) 11: [ RUN ] StringUtilityTest.SplitString 11: [ OK ] StringUtilityTest.SplitString (0 ms) 11: [ RUN ] StringUtilityTest.SplitDelimitedString 11: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 11: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 11: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 11: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 11: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 11: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 11: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 11: [----------] 9 tests from StringUtilityTest (0 ms total) 11: 11: [----------] 2 tests from FormatStringTest 11: [ RUN ] FormatStringTest.HandlesBasicFormatting 11: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 11: [ RUN ] FormatStringTest.HandlesLongStrings 11: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 11: [----------] 2 tests from FormatStringTest (0 ms total) 11: 11: [----------] 1 test from StringFormatterTest 11: [ RUN ] StringFormatterTest.HandlesBasicFormatting 11: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 11: [----------] 1 test from StringFormatterTest (0 ms total) 11: 11: [----------] 1 test from formatAndJoinTest 11: [ RUN ] formatAndJoinTest.Works 11: [ OK ] formatAndJoinTest.Works (0 ms) 11: [----------] 1 test from formatAndJoinTest (0 ms total) 11: 11: [----------] 1 test from JoinStringsTest 11: [ RUN ] JoinStringsTest.Works 11: [ OK ] JoinStringsTest.Works (0 ms) 11: [----------] 1 test from JoinStringsTest (0 ms total) 11: 11: [----------] 6 tests from ReplaceAllTest 11: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 11: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesNoMatches 11: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 11: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 11: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 11: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 11: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 11: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 11: [----------] 6 tests from ReplaceAllTest (0 ms total) 11: 11: [----------] 10 tests from TextLineWrapperTest 11: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 11: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 11: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 11: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 11: [ RUN ] TextLineWrapperTest.WrapsCorrectly 11: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 11: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 11: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesIndent 11: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 11: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 11: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 11: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 11: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 11: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 11: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 11: [----------] 10 tests from TextLineWrapperTest (0 ms total) 11: 11: [----------] 3 tests from TemplateMPTest 11: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 11: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 11: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 11: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 11: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 11: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 11: [----------] 3 tests from TemplateMPTest (0 ms total) 11: 11: [----------] 6 tests from TextWriterTest 11: [ RUN ] TextWriterTest.WritesLines 11: [ OK ] TextWriterTest.WritesLines (0 ms) 11: [ RUN ] TextWriterTest.WritesLinesInParts 11: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 11: [ RUN ] TextWriterTest.WritesWrappedLines 11: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 11: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 11: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 11: [ RUN ] TextWriterTest.TracksNewlines 11: [ OK ] TextWriterTest.TracksNewlines (0 ms) 11: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 11: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 11: [----------] 6 tests from TextWriterTest (0 ms total) 11: 11: [----------] 1 test from TypeTraitsTest 11: [ RUN ] TypeTraitsTest.IsIntegralConstant 11: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 11: [----------] 1 test from TypeTraitsTest (0 ms total) 11: 11: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 11: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 11: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 11: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 11: 11: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 11: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 11: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 11: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 11: 11: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 11: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 11: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 11: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 11: 11: [----------] 11 tests from WithInputPaths/PathSearchTest 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 11: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 11: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 11: [----------] 11 tests from WithInputPaths/PathSearchTest (1 ms total) 11: 11: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 11: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 11: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 11: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 386 tests from 61 test suites ran. (12 ms total) 11: [ PASSED ] 386 tests. 11: 11: YOU HAVE 1 DISABLED TEST 11: 11/81 Test #11: UtilityUnitTests ............................... Passed 0.51 sec test 12 Start 12: UtilityMpiUnitTests 12: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/utility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/UtilityMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/utility/tests 12: Test timeout computed to be: 30 12: [==========] Running 2 tests from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 2 tests from PhysicalNodeCommunicatorTest 12: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 12: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms) 12: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 12: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 12: [----------] 2 tests from PhysicalNodeCommunicatorTest (2 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 2 tests from 1 test suite ran. (2 ms total) 12: [ PASSED ] 2 tests. 12/81 Test #12: UtilityMpiUnitTests ............................ Passed 0.44 sec test 13 Start 13: GmxlibTests 13: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/GmxlibTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxlib/nonbonded/tests 13: Test timeout computed to be: 30 13: [==========] Running 72 tests from 1 test suite. 13: [----------] Global test environment set-up. 13: [----------] 72 tests from NBInteraction/NonbondedFepTest 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 13: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 13: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 13: [----------] 72 tests from NBInteraction/NonbondedFepTest (12 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 72 tests from 1 test suite ran. (12 ms total) 13: [ PASSED ] 72 tests. 13/81 Test #13: GmxlibTests .................................... Passed 0.52 sec test 14 Start 14: MdlibUnitTest 14: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdlibUnitTest.xml" 14: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests 14: Test timeout computed to be: 30 14: [==========] Running 155 tests from 17 test suites. 14: [----------] Global test environment set-up. 14: [----------] 1 test from VerletBufferConstraintTest 14: [ RUN ] VerletBufferConstraintTest.EqualMasses 14: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 14: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 14: 14: [----------] 6 tests from CalcvirTest 14: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 14: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 14: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 14: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 14: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 14: [----------] 6 tests from CalcvirTest (0 ms total) 14: 14: [----------] 2 tests from PrEbinTest 14: [ RUN ] PrEbinTest.HandlesAverages 14: [ OK ] PrEbinTest.HandlesAverages (0 ms) 14: [ RUN ] PrEbinTest.HandlesEmptyAverages 14: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 14: [----------] 2 tests from PrEbinTest (0 ms total) 14: 14: [----------] 3 tests from EnergyDriftTracker 14: [ RUN ] EnergyDriftTracker.emptyWorks 14: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 14: [ RUN ] EnergyDriftTracker.onePointWorks 14: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 14: [ RUN ] EnergyDriftTracker.manyPointsWorks 14: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 14: [----------] 3 tests from EnergyDriftTracker (0 ms total) 14: 14: [----------] 4 tests from ShakeTest 14: [ RUN ] ShakeTest.ConstrainsOneBond 14: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 14: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 14: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 14: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 14: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 14: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 14: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 14: [----------] 4 tests from ShakeTest (0 ms total) 14: 14: [----------] 1 test from NullSignalTest 14: [ RUN ] NullSignalTest.NullSignallerWorks 14: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 14: [----------] 1 test from NullSignalTest (0 ms total) 14: 14: [----------] 7 tests from SignalTest 14: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 14: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 14: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 14: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 14: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 14: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 14: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 14: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 14: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 14: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 14: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 14: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 14: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 14: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 14: [----------] 7 tests from SignalTest (0 ms total) 14: 14: [----------] 13 tests from UpdateGroupsTest 14: [ RUN ] UpdateGroupsTest.WithEthaneUA 14: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 14: [ RUN ] UpdateGroupsTest.WithMethane 14: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 14: [ RUN ] UpdateGroupsTest.WithEthane 14: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 14: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 14: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 14: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 14: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 14: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 14: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 14: [ RUN ] UpdateGroupsTest.WithWaterFourSite 14: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 14: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 14: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 14: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 14: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 14: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 14: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 14: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 14: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 14: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 14: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 14: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 14: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 14: [----------] 13 tests from UpdateGroupsTest (1 ms total) 14: 14: [----------] 1 test from UpdateGroupsCog 14: [ RUN ] UpdateGroupsCog.ComputesCogs 14: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 14: [----------] 1 test from UpdateGroupsCog (0 ms total) 14: 14: [----------] 2 tests from WholeMoleculeTransform 14: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 14: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 14: [ RUN ] WholeMoleculeTransform.HandlesReordering 14: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 14: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 14: 14: [----------] 14 tests from WithParameters/ConstraintsTest 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (7 ms) 14: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 14: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (5 ms) 14: [----------] 14 tests from WithParameters/ConstraintsTest (18 ms total) 14: 14: [----------] 11 tests from WithParameters/EnergyOutputTest 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 14: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (1 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 14: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 14: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (1 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 14: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 14: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 14: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (5 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 14: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (1 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 14: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (1 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 14: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (1 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 14: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (1 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 14: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (1 ms) 14: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 14: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 14: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (1 ms) 14: [----------] 11 tests from WithParameters/EnergyOutputTest (22 ms total) 14: 14: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 14: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 14: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 14: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 14: 14: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 14: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 14: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 14: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 14: 14: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 14: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 14: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 14: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 14: 14: [----------] 16 tests from WithParameters/LeapFrogTest 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (1 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (4 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (1 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (1 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (1 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (1 ms) 14: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 14: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 14: [----------] 16 tests from WithParameters/LeapFrogTest (20 ms total) 14: 14: [----------] 13 tests from WithParameters/SettleTest 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) 14: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 14: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (1 ms) 14: [----------] 13 tests from WithParameters/SettleTest (8 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 155 tests from 17 test suites ran. (74 ms total) 14: [ PASSED ] 155 tests. 14/81 Test #14: MdlibUnitTest .................................. Passed 0.65 sec test 15 Start 15: AwhTest 15: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/AwhTest.xml" 15: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/awh/tests 15: Test timeout computed to be: 30 15: [==========] Running 20 tests from 7 test suites. 15: [----------] Global test environment set-up. 15: [----------] 3 tests from SerializationTest 15: [ RUN ] SerializationTest.CanSerializeDimParams 15: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 15: [ RUN ] SerializationTest.CanSerializeBiasParams 15: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 15: [ RUN ] SerializationTest.CanSerializeAwhParams 15: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 15: [----------] 3 tests from SerializationTest (0 ms total) 15: 15: [----------] 1 test from BiasTest 15: [ RUN ] BiasTest.DetectsCovering 15: [ OK ] BiasTest.DetectsCovering (0 ms) 15: [----------] 1 test from BiasTest (0 ms total) 15: 15: [----------] 1 test from biasGridTest 15: [ RUN ] biasGridTest.neighborhood 15: [ OK ] biasGridTest.neighborhood (1 ms) 15: [----------] 1 test from biasGridTest (1 ms total) 15: 15: [----------] 1 test from BiasFepLambdaStateTest 15: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 15: [ OK ] BiasFepLambdaStateTest.DetectsCovering (3 ms) 15: [----------] 1 test from BiasFepLambdaStateTest (3 ms total) 15: 15: [----------] 8 tests from WithParameters/BiasTest 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (0 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms) 15: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 15: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms) 15: [----------] 8 tests from WithParameters/BiasTest (4 ms total) 15: 15: [----------] 2 tests from WithParameters/BiasStateTest 15: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 15: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 15: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 15: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 15: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 15: 15: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (8 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (7 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (7 ms) 15: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 15: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (8 ms) 15: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (34 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 20 tests from 7 test suites ran. (46 ms total) 15: [ PASSED ] 20 tests. 15/81 Test #15: AwhTest ........................................ Passed 0.52 sec test 16 Start 16: DensityFittingAppliedForcesUnitTest 16: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/densityfitting/tests 16: Test timeout computed to be: 30 16: [==========] Running 18 tests from 4 test suites. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from DensityFittingTest 16: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 16: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 16: [ RUN ] DensityFittingTest.SingleAtom 16: [ OK ] DensityFittingTest.SingleAtom (0 ms) 16: [----------] 2 tests from DensityFittingTest (0 ms total) 16: 16: [----------] 7 tests from DensityFittingAmplitudeLookupTest 16: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 16: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 16: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 16: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 16: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 16: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 16: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 16: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 16: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 16: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 16: 16: [----------] 1 test from DensityFittingForceProviderState 16: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 16: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 16: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 16: 16: [----------] 8 tests from DensityFittingOptionsTest 16: [ RUN ] DensityFittingOptionsTest.DefaultParameters 16: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 16: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 16: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 16: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 16: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 16: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 16: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 16: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 16: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 16: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 16: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 16: [ RUN ] DensityFittingOptionsTest.KvtToInternal 16: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 16: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 16: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 16: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 18 tests from 4 test suites ran. (1 ms total) 16: [ PASSED ] 18 tests. 16/81 Test #16: DensityFittingAppliedForcesUnitTest ............ Passed 0.48 sec test 17 Start 17: QMMMAppliedForcesUnitTest 17: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests 17: Test timeout computed to be: 30 17: [==========] Running 21 tests from 5 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from QMMMInputGeneratorTest 17: [ RUN ] QMMMInputGeneratorTest.CanConstruct 17: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 17: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 17: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 17: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 17: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 17: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 17: 17: [----------] 7 tests from QMMMTopologyPreprocessorTest 17: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 17: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 21.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to -1143642705 17: 17: Generated 10 of the 10 non-bonded parameter combinations 17: 17: Generated 10 of the 10 1-4 parameter combinations 17: 17: Excluding 2 bonded neighbours molecule type 'SOL' 17: Analysing residue names: 17: There are: 4 Water residues 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (5 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 21.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to 804532095 17: 17: Generated 10 of the 10 non-bonded parameter combinations 17: 17: Generated 10 of the 10 1-4 parameter combinations 17: 17: Excluding 2 bonded neighbours molecule type 'SOL' 17: Analysing residue names: 17: There are: 4 Water residues 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (4 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 21.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to -1073913985 17: 17: Generated 10 of the 10 non-bonded parameter combinations 17: 17: Generated 10 of the 10 1-4 parameter combinations 17: 17: Excluding 2 bonded neighbours molecule type 'SOL' 17: Analysing residue names: 17: There are: 4 Water residues 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (4 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: Number of degrees of freedom in T-Coupling group rest is 63.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 17: NVE simulation: will use the initial temperature of 129.093 K for 17: determining the Verlet buffer size 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to -1175527450 17: 17: Generated 2145 of the 2145 non-bonded parameter combinations 17: 17: Generated 2145 of the 2145 1-4 parameter combinations 17: 17: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 17: Analysing residue names: 17: There are: 3 Protein residues 17: Analysing Protein... 17: 17: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 17: 17: Calculated rlist for 1x1 atom pair-list as 1.013 nm, buffer size 0.013 nm 17: 17: Set rlist, assuming 4x4 atom pair-list, to 1.008 nm, buffer size 0.008 nm 17: 17: Note that mdrun will redetermine rlist based on the actual pair-list setup 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (15 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Generating 1-4 interactions: fudge = 0.5 17: 17: NOTE 2 [file unknown]: 17: You are using constraints on all bonds, whereas the forcefield has been 17: parametrized only with constraints involving hydrogen atoms. We suggest 17: using constraints = h-bonds instead, this will also improve performance. 17: 17: 17: NOTE 3 [file unknown]: 17: For energy conservation with LINCS, lincs_iter should be 2 or larger. 17: 17: 17: Number of degrees of freedom in T-Coupling group rest is 42.00 17: 17: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 17: NVE simulation: will use the initial temperature of 193.640 K for 17: determining the Verlet buffer size 17: 17: 17: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 5 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to -345065569 17: 17: Generated 2145 of the 2145 non-bonded parameter combinations 17: 17: Generated 2145 of the 2145 1-4 parameter combinations 17: 17: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 17: 17: turning all bonds into constraints... 17: Analysing residue names: 17: There are: 3 Protein residues 17: Analysing Protein... 17: 17: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 17: 17: Calculated rlist for 1x1 atom pair-list as 1.015 nm, buffer size 0.015 nm 17: 17: Set rlist, assuming 4x4 atom pair-list, to 1.009 nm, buffer size 0.009 nm 17: 17: Note that mdrun will redetermine rlist based on the actual pair-list setup 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (16 ms) 17: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 17: 17: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 17: For a correct single-point energy evaluation with nsteps = 0, use 17: continuation = yes to avoid constraining the input coordinates. 17: 17: Number of degrees of freedom in T-Coupling group rest is 45.00 17: 17: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 17: NVE simulation with an initial temperature of zero: will use a Verlet 17: buffer of 10%. Check your energy drift! 17: 17: 17: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 17: You are using a plain Coulomb cut-off, which might produce artifacts. 17: You might want to consider using PME electrostatics. 17: 17: 17: 17: There were 3 notes 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 17: Setting the LD random seed to 2113376111 17: 17: Generated 3 of the 6 non-bonded parameter combinations 17: 17: Excluding 3 bonded neighbours molecule type 'VSTEST' 17: 17: Cleaning up constraints and constant bonded interactions with virtual sites 17: Analysing residue names: 17: There are: 1 Other residues 17: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 17: 17: This run will generate roughly 0 Mb of data 17: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (5 ms) 17: [----------] 7 tests from QMMMTopologyPreprocessorTest (50 ms total) 17: 17: [----------] 9 tests from QMMMOptionsTest 17: [ RUN ] QMMMOptionsTest.DefaultParameters 17: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 17: [ RUN ] QMMMOptionsTest.OptionSetsActive 17: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 17: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 17: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 17: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 17: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 17: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 17: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 17: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 17: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 17: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 17: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 17: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 17: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 17: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 17: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 17: [----------] 9 tests from QMMMOptionsTest (2 ms total) 17: 17: [----------] 1 test from QMMMForceProviderTest 17: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 17: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 17: [----------] 1 test from QMMMForceProviderTest (0 ms total) 17: 17: [----------] 1 test from QMMMTest 17: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 17: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 17: [----------] 1 test from QMMMTest (0 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 21 tests from 5 test suites ran. (53 ms total) 17: [ PASSED ] 21 tests. 17/81 Test #17: QMMMAppliedForcesUnitTest ...................... Passed 0.57 sec test 18 Start 18: AppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/AppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/applied_forces/tests 18: Test timeout computed to be: 30 18: [==========] Running 3 tests from 1 test suite. 18: [----------] Global test environment set-up. 18: [----------] 3 tests from ElectricFieldTest 18: [ RUN ] ElectricFieldTest.Static 18: [ OK ] ElectricFieldTest.Static (0 ms) 18: [ RUN ] ElectricFieldTest.Oscillating 18: [ OK ] ElectricFieldTest.Oscillating (0 ms) 18: [ RUN ] ElectricFieldTest.Pulsed 18: [ OK ] ElectricFieldTest.Pulsed (0 ms) 18: [----------] 3 tests from ElectricFieldTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 3 tests from 1 test suite ran. (0 ms total) 18: [ PASSED ] 3 tests. 18/81 Test #18: AppliedForcesUnitTest .......................... Passed 0.48 sec test 19 Start 19: ListedForcesTest 19: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/ListedForcesTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/listed_forces/tests 19: Test timeout computed to be: 30 19: [==========] Running 132 tests from 9 test suites. 19: [----------] Global test environment set-up. 19: [----------] 24 tests from Bond/ListedForcesTest 19: [ RUN ] Bond/ListedForcesTest.Ifunc/0 19: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/1 19: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/2 19: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/3 19: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/4 19: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/5 19: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/6 19: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/7 19: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/8 19: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/9 19: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/10 19: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/11 19: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/12 19: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/13 19: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/14 19: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/15 19: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/16 19: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/17 19: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/18 19: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/19 19: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/20 19: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/21 19: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/22 19: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 19: [ RUN ] Bond/ListedForcesTest.Ifunc/23 19: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 19: [----------] 24 tests from Bond/ListedForcesTest (4 ms total) 19: 19: [----------] 33 tests from Angle/ListedForcesTest 19: [ RUN ] Angle/ListedForcesTest.Ifunc/0 19: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/1 19: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/2 19: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/3 19: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/4 19: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/5 19: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/6 19: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/7 19: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/8 19: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/9 19: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/10 19: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/11 19: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/12 19: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/13 19: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/14 19: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/15 19: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/16 19: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/17 19: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/18 19: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/19 19: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/20 19: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/21 19: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/22 19: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/23 19: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/24 19: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/25 19: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/26 19: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/27 19: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/28 19: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/29 19: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/30 19: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/31 19: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 19: [ RUN ] Angle/ListedForcesTest.Ifunc/32 19: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 19: [----------] 33 tests from Angle/ListedForcesTest (7 ms total) 19: 19: [----------] 18 tests from Dihedral/ListedForcesTest 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (1 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 19: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 19: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 19: [----------] 18 tests from Dihedral/ListedForcesTest (4 ms total) 19: 19: [----------] 12 tests from Polarize/ListedForcesTest 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 19: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 19: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 19: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 19: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 19: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 19: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 19: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 19: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 19: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 19: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 19: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 19: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 19: [----------] 12 tests from Polarize/ListedForcesTest (1 ms total) 19: 19: [----------] 18 tests from Restraints/ListedForcesTest 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 19: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 19: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 19: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 19: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 19: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 19: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 19: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 19: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 19: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 19: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 19: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 19: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 19: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 19: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 19: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 19: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 19: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 19: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 19: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 19: [----------] 18 tests from Restraints/ListedForcesTest (3 ms total) 19: 19: [----------] 3 tests from BondZeroLength/ListedForcesTest 19: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 19: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 19: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 19: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 19: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 19: 19: [----------] 3 tests from AngleZero/ListedForcesTest 19: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 19: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 19: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 19: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 19: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 19: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 19: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 19: 19: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 19: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 19: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 19: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (3 ms total) 19: 19: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 19: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 19: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 19: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (1 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 132 tests from 9 test suites ran. (27 ms total) 19: [ PASSED ] 132 tests. 19/81 Test #19: ListedForcesTest ............................... Passed 0.51 sec test 20 Start 20: NbnxmTests 20: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/NbnxmTests.xml" 20: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/nbnxm/tests 20: Test timeout computed to be: 30 20: [==========] Running 18 tests from 1 test suite. 20: [----------] Global test environment set-up. 20: [----------] 18 tests from KernelSetupTest 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 20: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 20: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 20: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 20: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 20: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 20: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 20: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 20: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 20: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 20: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 20: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 20: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 20: [----------] 18 tests from KernelSetupTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 18 tests from 1 test suite ran. (0 ms total) 20: [ PASSED ] 18 tests. 20/81 Test #20: NbnxmTests ..................................... Passed 0.46 sec test 21 Start 21: CommandLineUnitTests 21: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/CommandLineUnitTests.xml" 21: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/commandline/tests 21: Test timeout computed to be: 30 21: [==========] Running 60 tests from 7 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from CommandLineHelpModuleTest 21: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 21: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 21: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 21: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 21: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 21: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 21: [----------] 3 tests from CommandLineHelpModuleTest (1 ms total) 21: 21: [----------] 7 tests from CommandLineHelpWriterTest 21: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 21: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 21: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 21: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 21: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 21: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 21: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 21: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 21: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 21: [----------] 7 tests from CommandLineHelpWriterTest (1 ms total) 21: 21: [----------] 6 tests from CommandLineModuleManagerTest 21: [ RUN ] CommandLineModuleManagerTest.RunsModule 21: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 21: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 21: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 21: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 21: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 21: 21: [----------] 13 tests from CommandLineParserTest 21: [ RUN ] CommandLineParserTest.HandlesSingleValues 21: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 21: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 21: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 21: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 21: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 21: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesString 21: [ OK ] CommandLineParserTest.HandlesString (0 ms) 21: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 21: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 21: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 21: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 21: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 21: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 21: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 21: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 21: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 21: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 21: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 21: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 21: [----------] 13 tests from CommandLineParserTest (0 ms total) 21: 21: [----------] 6 tests from CommandLineProgramContextTest 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 21: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 21: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 21: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 21: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 21: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 21: 21: [----------] 3 tests from OutputNamesTest 21: [ RUN ] OutputNamesTest.CanBeSuffixed 21: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 21: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 21: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 21: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 21: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 21: [----------] 3 tests from OutputNamesTest (0 ms total) 21: 21: [----------] 22 tests from ParseCommonArgsTest 21: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 21: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 21: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 21: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 21: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 21: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 21: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 21: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 21: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 21: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 21: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 21: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 21: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 21: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 21: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 21: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 21: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 21: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 21: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 21: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 21: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 21: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 21: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 21: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 21: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 21: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 21: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 21: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 21: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 21: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 21: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 21: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 21: [----------] 22 tests from ParseCommonArgsTest (3 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 60 tests from 7 test suites ran. (8 ms total) 21: [ PASSED ] 60 tests. 21/81 Test #21: CommandLineUnitTests ........................... Passed 0.49 sec test 22 Start 22: DomDecTests 22: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/DomDecTests.xml" 22: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests 22: Test timeout computed to be: 30 22: [==========] Running 9 tests from 2 test suites. 22: [----------] Global test environment set-up. 22: [----------] 7 tests from HashedMap 22: [ RUN ] HashedMap.InsertsFinds 22: [ OK ] HashedMap.InsertsFinds (0 ms) 22: [ RUN ] HashedMap.NegativeKeysWork 22: [ OK ] HashedMap.NegativeKeysWork (0 ms) 22: [ RUN ] HashedMap.InsertsErases 22: [ OK ] HashedMap.InsertsErases (0 ms) 22: [ RUN ] HashedMap.InsertsOrAssigns 22: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 22: [ RUN ] HashedMap.Clears 22: [ OK ] HashedMap.Clears (0 ms) 22: [ RUN ] HashedMap.LinkedEntries 22: [ OK ] HashedMap.LinkedEntries (0 ms) 22: [ RUN ] HashedMap.ResizesTable 22: [ OK ] HashedMap.ResizesTable (0 ms) 22: [----------] 7 tests from HashedMap (0 ms total) 22: 22: [----------] 2 tests from LocalAtomSetManager 22: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 22: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 22: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 22: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 22: [----------] 2 tests from LocalAtomSetManager (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 9 tests from 2 test suites ran. (0 ms total) 22: [ PASSED ] 9 tests. 22/81 Test #22: DomDecTests .................................... Passed 0.49 sec test 23 Start 23: DomDecMpiTests 23: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/domdec-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/DomDecMpiTests.xml" 23: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/domdec/tests 23: Test timeout computed to be: 30 23: [==========] Running 4 tests from 1 test suite. 23: [----------] Global test environment set-up. 23: [----------] 4 tests from HaloExchangeTest 23: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 23: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (0 ms) 23: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 23: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (0 ms) 23: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 23: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (0 ms) 23: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 23: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (0 ms) 23: [----------] 4 tests from HaloExchangeTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 4 tests from 1 test suite ran. (0 ms total) 23: [ PASSED ] 4 tests. 23/81 Test #23: DomDecMpiTests ................................. Passed 0.61 sec test 24 Start 24: EwaldUnitTests 24: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/EwaldUnitTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/ewald/tests 24: Test timeout computed to be: 30 24: [==========] Running 407 tests from 9 test suites. 24: [----------] Global test environment set-up. 24: [----------] 6 tests from SeparatePmeRanksPermittedTest 24: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 24: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 24: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 24: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 24: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 24: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 24: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 24: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 24: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 24: 24: [----------] 108 tests from Pme_SplineAndSpreadTest 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (4 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (3 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (1 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 24: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 24: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (4 ms) 24: [----------] 108 tests from Pme_SplineAndSpreadTest (160 ms total) 24: 24: [----------] 64 tests from Pme_SolveTest 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [----------] 64 tests from Pme_SolveTest (23 ms total) 24: 24: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (7 ms total) 24: 24: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 24: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (13 ms total) 24: 24: [----------] 64 tests from PmeDiffEps_SolveTest 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (1 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 24: Test is being skipped because: 24: CPU PME solve does not implement XYZ grid ordering 24: 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 24: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 24: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 24: [----------] 64 tests from PmeDiffEps_SolveTest (22 ms total) 24: 24: [----------] 72 tests from Pme_GatherTest 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 24: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 24: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 24: [----------] 72 tests from Pme_GatherTest (28 ms total) 24: 24: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (2 ms) 24: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 24: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 24: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (3 ms total) 24: 24: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (6 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 24: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 24: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 24: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (53 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 407 tests from 9 test suites ran. (312 ms total) 24: [ PASSED ] 311 tests. 24: [ SKIPPED ] 96 tests, listed below: 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 24: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 24/81 Test #24: EwaldUnitTests ................................. Passed 0.93 sec test 25 Start 25: FFTUnitTests 25: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/FFTUnitTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fft/tests 25: Test timeout computed to be: 1920 25: [==========] Running 15 tests from 4 test suites. 25: [----------] Global test environment set-up. 25: [----------] 2 tests from ManyFFTTest 25: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 25: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (10 ms) 25: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 25: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (29 ms) 25: [----------] 2 tests from ManyFFTTest (40 ms total) 25: 25: [----------] 1 test from FFTTest 25: [ RUN ] FFTTest.Real2DLength18_15Test 25: [ OK ] FFTTest.Real2DLength18_15Test (6 ms) 25: [----------] 1 test from FFTTest (7 ms total) 25: 25: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (5 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (18 ms) 25: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 25: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (26 ms) 25: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (59 ms total) 25: 25: [----------] 2 tests from Works/ParameterizedFFTTest3D 25: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 25: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (1 ms) 25: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 25: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (2 ms) 25: [----------] 2 tests from Works/ParameterizedFFTTest3D (4 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 15 tests from 4 test suites ran. (112 ms total) 25: [ PASSED ] 15 tests. 25/81 Test #25: FFTUnitTests ................................... Passed 0.69 sec test 26 Start 26: GpuUtilsUnitTests 26: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/GpuUtilsUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gpu_utils/tests 26: Test timeout computed to be: 30 26: [==========] Running 64 tests from 22 test suites. 26: [----------] Global test environment set-up. 26: [----------] 2 tests from ClfftInitializer 26: [ RUN ] ClfftInitializer.SingleInitializationWorks 26: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 26: [ RUN ] ClfftInitializer.TwoInitializationsWork 26: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 26: [----------] 2 tests from ClfftInitializer (0 ms total) 26: 26: [----------] 1 test from DevicesAvailable 26: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 26: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 26: [----------] 1 test from DevicesAvailable (0 ms total) 26: 26: [----------] 1 test from DeviceStreamManagerTest 26: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 26: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 26: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 26: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 26: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 26: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 26: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 26: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 26: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 26: 26: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 26: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 26: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 26: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 26: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 26: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 26: 26: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 26: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 26: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 26: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 26: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 26: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 26: 26: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 26: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 26: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 26: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 26: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 26: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 26: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 26: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.Swap 26: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/0.Comparison 26: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 26: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 26: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.Swap 26: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/1.Comparison 26: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 26: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.Swap 26: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/2.Comparison 26: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 26: 26: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 26: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 26: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 26: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 26: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.Swap 26: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 26: [ RUN ] HostAllocatorTestNoMem/3.Comparison 26: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 26: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 26: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 26: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 26: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 26: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 26: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 26: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 26: 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 26: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 26: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 26: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 26: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 26: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 26: 26: [----------] 1 test from HostAllocatorUntypedTest 26: [ RUN ] HostAllocatorUntypedTest.Comparison 26: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 26: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 26: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/0.Move 26: [ OK ] AllocatorTest/0.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/0 (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 26: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/1.Move 26: [ OK ] AllocatorTest/1.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/1 (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 26: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/2.Move 26: [ OK ] AllocatorTest/2.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/2 (0 ms total) 26: 26: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 26: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 26: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 26: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 26: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 26: [ RUN ] AllocatorTest/3.Move 26: [ OK ] AllocatorTest/3.Move (0 ms) 26: [----------] 4 tests from AllocatorTest/3 (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 64 tests from 22 test suites ran. (2 ms total) 26: [ PASSED ] 64 tests. 26/81 Test #26: GpuUtilsUnitTests .............................. Passed 0.55 sec test 27 Start 27: HardwareUnitTests 27: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/HardwareUnitTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/hardware/tests 27: Test timeout computed to be: 30 27: [==========] Running 21 tests from 9 test suites. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CpuInfoTest 27: [ RUN ] CpuInfoTest.SupportLevel 27: [ OK ] CpuInfoTest.SupportLevel (30 ms) 27: [----------] 1 test from CpuInfoTest (30 ms total) 27: 27: [----------] 4 tests from HardwareTopologyTest 27: [ RUN ] HardwareTopologyTest.Execute 27: [ OK ] HardwareTopologyTest.Execute (43 ms) 27: [ RUN ] HardwareTopologyTest.HwlocExecute 27: [ OK ] HardwareTopologyTest.HwlocExecute (40 ms) 27: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 27: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (44 ms) 27: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 27: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (51 ms) 27: [----------] 4 tests from HardwareTopologyTest (180 ms total) 27: 27: [----------] 1 test from DevicesManagerTest 27: [ RUN ] DevicesManagerTest.Serialization 27: [ OK ] DevicesManagerTest.Serialization (0 ms) 27: [----------] 1 test from DevicesManagerTest (0 ms total) 27: 27: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 27: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 27: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 27: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (6 ms total) 27: 27: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (1 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 27: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 27: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 27: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (4 ms total) 27: 27: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 27: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 27: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 27: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 27: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 27: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) 27: 27: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 27: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (1 ms) 27: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (1 ms total) 27: 27: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 27: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (2 ms) 27: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (2 ms total) 27: 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 27: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 27: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (16 ms) 27: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (17 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 21 tests from 9 test suites ran. (244 ms total) 27: [ PASSED ] 21 tests. 27/81 Test #27: HardwareUnitTests .............................. Passed 0.73 sec test 28 Start 28: MathUnitTests 28: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MathUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/math/tests 28: Test timeout computed to be: 30 28: [==========] Running 301 tests from 38 test suites. 28: [----------] Global test environment set-up. 28: [----------] 1 test from EmptyArrayRefWithPaddingTest 28: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 28: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 28: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 28: 28: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 28: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 28: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 28: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 28: 28: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 28: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 28: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 28: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 28: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 28: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 28: 28: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 28: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 28: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 28: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 28: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 28: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 28: 28: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 28: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 28: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 28: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 28: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 28: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 28: 28: [----------] 11 tests from TranslateAndScaleTest 28: [ RUN ] TranslateAndScaleTest.identityTransformation 28: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 28: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 28: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 28: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 28: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 28: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 28: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 28: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingIdentity 28: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 28: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 28: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 28: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 28: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 28: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 28: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 28: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 28: 28: [----------] 3 tests from AffineTransformationTest 28: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 28: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 28: [ RUN ] AffineTransformationTest.applyTransformationToVectors 28: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 28: [ RUN ] AffineTransformationTest.retrieveGradient 28: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 28: [----------] 3 tests from AffineTransformationTest (0 ms total) 28: 28: [----------] 12 tests from DensitySimilarityTest 28: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 28: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 28: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 28: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 28: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 28: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 28: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 28: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 28: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 28: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 28: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 28: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 28: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (32 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (31 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (2 ms) 28: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 28: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 28: [----------] 12 tests from DensitySimilarityTest (67 ms total) 28: 28: [----------] 6 tests from StructureSimilarityTest 28: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 28: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 28: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 28: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 28: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 28: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 28: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 28: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 28: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 28: [----------] 6 tests from StructureSimilarityTest (0 ms total) 28: 28: [----------] 8 tests from ExponentialMovingAverage 28: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 28: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 28: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 28: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 28: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 28: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 28: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 28: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 28: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 28: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 28: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 28: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 28: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 28: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 28: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 28: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 28: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 28: 28: [----------] 21 tests from FunctionTest 28: [ RUN ] FunctionTest.StaticLog2 28: [ OK ] FunctionTest.StaticLog2 (0 ms) 28: [ RUN ] FunctionTest.Log2I32Bit 28: [ OK ] FunctionTest.Log2I32Bit (0 ms) 28: [ RUN ] FunctionTest.Log2I64Bit 28: [ OK ] FunctionTest.Log2I64Bit (0 ms) 28: [ RUN ] FunctionTest.GreatestCommonDivisor 28: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 28: [ RUN ] FunctionTest.InvsqrtFloat 28: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 28: [ RUN ] FunctionTest.InvsqrtDouble 28: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 28: [ RUN ] FunctionTest.InvsqrtInteger 28: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 28: [ RUN ] FunctionTest.InvcbrtFloat 28: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 28: [ RUN ] FunctionTest.InvcbrtDouble 28: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 28: [ RUN ] FunctionTest.InvcbrtInteger 28: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 28: [ RUN ] FunctionTest.SixthrootFloat 28: [ OK ] FunctionTest.SixthrootFloat (0 ms) 28: [ RUN ] FunctionTest.SixthrootDouble 28: [ OK ] FunctionTest.SixthrootDouble (0 ms) 28: [ RUN ] FunctionTest.SixthrootInteger 28: [ OK ] FunctionTest.SixthrootInteger (0 ms) 28: [ RUN ] FunctionTest.InvsixthrootFloat 28: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 28: [ RUN ] FunctionTest.InvsixthrootDouble 28: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 28: [ RUN ] FunctionTest.InvsixthrootInteger 28: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 28: [ RUN ] FunctionTest.Powers 28: [ OK ] FunctionTest.Powers (0 ms) 28: [ RUN ] FunctionTest.ErfInvFloat 28: [ OK ] FunctionTest.ErfInvFloat (0 ms) 28: [ RUN ] FunctionTest.ErfInvDouble 28: [ OK ] FunctionTest.ErfInvDouble (0 ms) 28: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 28: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 28: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 28: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 28: [----------] 21 tests from FunctionTest (2 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/0, where TypeParam = char 28: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/0 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 28: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/1 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/2, where TypeParam = int 28: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/2 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/3, where TypeParam = unsigned int 28: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/3 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/4, where TypeParam = long 28: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/4 (0 ms total) 28: 28: [----------] 1 test from FunctionTestIntegerTypes/5, where TypeParam = unsigned long 28: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 28: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 28: [----------] 1 test from FunctionTestIntegerTypes/5 (0 ms total) 28: 28: [----------] 4 tests from GaussianOn1DLattice 28: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 28: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 28: [ RUN ] GaussianOn1DLattice.isCorrect 28: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 28: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 28: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 28: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 28: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 28: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 28: 28: [----------] 9 tests from GaussTransformTest 28: [ RUN ] GaussTransformTest.isZeroUponConstruction 28: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 28: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 28: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 28: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 28: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 28: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 28: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 28: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 28: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 28: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 28: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 28: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 28: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 28: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 28: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 28: [ RUN ] GaussTransformTest.view 28: [ OK ] GaussTransformTest.view (0 ms) 28: [----------] 9 tests from GaussTransformTest (0 ms total) 28: 28: [----------] 3 tests from DensityFittingForce 28: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 28: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 28: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 28: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 28: [ RUN ] DensityFittingForce.pullsTowardsDerivative 28: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 28: [----------] 3 tests from DensityFittingForce (0 ms total) 28: 28: [----------] 2 tests from InvertMatrixTest 28: [ RUN ] InvertMatrixTest.IdentityIsImpotent 28: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 28: [ RUN ] InvertMatrixTest.ComputesInverse 28: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 28: [----------] 2 tests from InvertMatrixTest (0 ms total) 28: 28: [----------] 2 tests from InvertBoxMatrixTest 28: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 28: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 28: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 28: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 28: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 28: 28: [----------] 17 tests from MatrixTest 28: [ RUN ] MatrixTest.canSetFromArray 28: [ OK ] MatrixTest.canSetFromArray (0 ms) 28: [ RUN ] MatrixTest.canSetStaticallyFromList 28: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 28: [ RUN ] MatrixTest.canConstructAndFill 28: [ OK ] MatrixTest.canConstructAndFill (0 ms) 28: [ RUN ] MatrixTest.canSetValues 28: [ OK ] MatrixTest.canSetValues (0 ms) 28: [ RUN ] MatrixTest.canCopyAssign 28: [ OK ] MatrixTest.canCopyAssign (0 ms) 28: [ RUN ] MatrixTest.canSwap 28: [ OK ] MatrixTest.canSwap (0 ms) 28: [ RUN ] MatrixTest.staticMultiDimArrayExtent 28: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 28: [ RUN ] MatrixTest.determinantWorks 28: [ OK ] MatrixTest.determinantWorks (0 ms) 28: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 28: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 28: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 28: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 28: [ RUN ] MatrixTest.traceWorks 28: [ OK ] MatrixTest.traceWorks (0 ms) 28: [ RUN ] MatrixTest.transposeWorks 28: [ OK ] MatrixTest.transposeWorks (0 ms) 28: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 28: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 28: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 28: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 28: [ RUN ] MatrixTest.canFillLegacyMatrix 28: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 28: [ RUN ] MatrixTest.IdentityMatrix 28: [ OK ] MatrixTest.IdentityMatrix (0 ms) 28: [ RUN ] MatrixTest.MatrixVectorMultiplication 28: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 28: [----------] 17 tests from MatrixTest (0 ms total) 28: 28: [----------] 25 tests from MultiDimArrayTest 28: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 28: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 28: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 28: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 28: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 28: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 28: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 28: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 28: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 28: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 28: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 28: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 28: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSwapStatic 28: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 28: [ RUN ] MultiDimArrayTest.canSwapDynamic 28: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 28: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 28: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 28: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 28: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 28: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 28: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 28: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 28: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 28: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 28: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 28: [ RUN ] MultiDimArrayTest.conversionToView 28: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 28: [ RUN ] MultiDimArrayTest.conversionToConstView 28: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 28: [ RUN ] MultiDimArrayTest.viewBegin 28: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 28: [ RUN ] MultiDimArrayTest.viewEnd 28: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 28: [ RUN ] MultiDimArrayTest.constViewConstBegin 28: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 28: [ RUN ] MultiDimArrayTest.constViewConstEnd 28: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 28: [----------] 25 tests from MultiDimArrayTest (0 ms total) 28: 28: [----------] 4 tests from MultiDimArrayToMdSpanTest 28: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 28: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 28: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 28: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 28: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 28: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 28: 28: [----------] 9 tests from NelderMeadSimplexTest 28: [ RUN ] NelderMeadSimplexTest.BestVertex 28: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 28: [ RUN ] NelderMeadSimplexTest.WorstVertex 28: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 28: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 28: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 28: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 28: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 28: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 28: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 28: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 28: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 28: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 28: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 28: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 28: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 28: [ RUN ] NelderMeadSimplexTest.OrientedLength 28: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 28: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 28: 28: [----------] 2 tests from NelderMead 28: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 28: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 28: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 28: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 28: [----------] 2 tests from NelderMead (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 28: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ResizeWorks 28: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ReserveWorks 28: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/0.CanCopyAssign 28: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/0.CanMoveAssign 28: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/0.CanSwap 28: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 28: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ResizeWorks 28: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ReserveWorks 28: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/1.CanCopyAssign 28: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/1.CanMoveAssign 28: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/1.CanSwap 28: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 28: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ResizeWorks 28: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ReserveWorks 28: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/2.CanCopyAssign 28: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/2.CanMoveAssign 28: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/2.CanSwap 28: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 28: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ResizeWorks 28: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ReserveWorks 28: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/3.CanCopyAssign 28: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/3.CanMoveAssign 28: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/3.CanSwap 28: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 28: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ResizeWorks 28: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ReserveWorks 28: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/4.CanCopyAssign 28: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/4.CanMoveAssign 28: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/4.CanSwap 28: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 28: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ResizeWorks 28: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ReserveWorks 28: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/5.CanCopyAssign 28: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/5.CanMoveAssign 28: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/5.CanSwap 28: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 28: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ResizeWorks 28: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ReserveWorks 28: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/6.CanCopyAssign 28: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/6.CanMoveAssign 28: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/6.CanSwap 28: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 28: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ResizeWorks 28: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ReserveWorks 28: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/7.CanCopyAssign 28: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/7.CanMoveAssign 28: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/7.CanSwap 28: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 28: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ResizeWorks 28: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ReserveWorks 28: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/8.CanCopyAssign 28: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/8.CanMoveAssign 28: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/8.CanSwap 28: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 28: 28: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 28: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 28: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ResizeWorks 28: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ReserveWorks 28: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 28: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 28: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 28: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 28: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 28: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 28: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 28: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 28: [ RUN ] PaddedVectorTest/9.CanCopyAssign 28: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 28: [ RUN ] PaddedVectorTest/9.CanMoveAssign 28: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 28: [ RUN ] PaddedVectorTest/9.CanSwap 28: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 28: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 28: 28: [----------] 39 tests from RVecTest 28: [ RUN ] RVecTest.CanBeStoredInVector 28: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 28: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 28: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 28: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 28: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 28: [ RUN ] RVecTest.WorksAsMutable_rvec 28: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 28: [ RUN ] RVecTest.WorksAs_rvec_Array 28: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 28: [ RUN ] RVecTest.ComparesEqual 28: [ OK ] RVecTest.ComparesEqual (0 ms) 28: [ RUN ] RVecTest.ComparesUnequal 28: [ OK ] RVecTest.ComparesUnequal (0 ms) 28: [ RUN ] RVecTest.CanAddRVecToRvec 28: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 28: [ RUN ] RVecTest.CanAddAssignRVecToRvec 28: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 28: [ RUN ] RVecTest.CanSubtractRVecFromRvec 28: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 28: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 28: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 28: [ RUN ] RVecTest.CanDotProductRVecByRvec 28: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 28: [ RUN ] RVecTest.CanCrossProductRVecByRvec 28: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 28: [ RUN ] RVecTest.CanDivideRVecInplace 28: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 28: [ RUN ] RVecTest.CanScaleRVec 28: [ OK ] RVecTest.CanScaleRVec (0 ms) 28: [ RUN ] RVecTest.CanDivideRVec 28: [ OK ] RVecTest.CanDivideRVec (0 ms) 28: [ RUN ] RVecTest.CanDoUnitvFromRVec 28: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 28: [ RUN ] RVecTest.CanSqLengthOfRVec 28: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanLengthOfRVec 28: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanCastToRVec 28: [ OK ] RVecTest.CanCastToRVec (0 ms) 28: [ RUN ] RVecTest.CanCastToDVec 28: [ OK ] RVecTest.CanCastToDVec (0 ms) 28: [ RUN ] RVecTest.CanLeftScalarMultiply 28: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 28: [ RUN ] RVecTest.CanRightScalarMultiply 28: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 28: [ RUN ] RVecTest.CanGetUnitvFromRVec 28: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 28: [ RUN ] RVecTest.CanGetSqLengthOfRVec 28: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanGetLengthOfRVec 28: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 28: [ RUN ] RVecTest.CanDoCrossProductOfRVec 28: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 28: [ RUN ] RVecTest.CanDoDotProductOfRVec 28: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 28: [ RUN ] RVecTest.CanScaleByVector 28: [ OK ] RVecTest.CanScaleByVector (0 ms) 28: [ RUN ] RVecTest.asIVec 28: [ OK ] RVecTest.asIVec (0 ms) 28: [ RUN ] RVecTest.elementWiseMin 28: [ OK ] RVecTest.elementWiseMin (0 ms) 28: [ RUN ] RVecTest.elementWiseMax 28: [ OK ] RVecTest.elementWiseMax (0 ms) 28: [ RUN ] RVecTest.WorksAs_dvec_Reference 28: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 28: [ RUN ] RVecTest.WorksAs_ivec_Reference 28: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 28: [ RUN ] RVecTest.WorksAs_rvec_Reference 28: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 28: [ RUN ] RVecTest.CopyConstructorWorks 28: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 28: [ RUN ] RVecTest.CopyAssignmentWorks 28: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 28: [ RUN ] RVecTest.MoveConstructorWorks 28: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 28: [ RUN ] RVecTest.MoveAssignmentWorks 28: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 28: [----------] 39 tests from RVecTest (0 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 301 tests from 38 test suites ran. (73 ms total) 28: [ PASSED ] 301 tests. 28/81 Test #28: MathUnitTests .................................. Passed 0.62 sec test 29 Start 29: MdrunUtilityUnitTests 29: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunUtilityUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests 29: Test timeout computed to be: 30 29: [==========] Running 17 tests from 1 test suite. 29: [----------] Global test environment set-up. 29: [----------] 17 tests from ThreadAffinityTest 29: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 29: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 29: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 29: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 29: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 29: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 29: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 29: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 29: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 29: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 29: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 29: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 29: NOTE: Affinity setting failed. 29: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 29: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 29: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 29: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 29: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 29: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 29: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 29: NOTE: Affinity setting for 1/2 threads failed. 29: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 29: [----------] 17 tests from ThreadAffinityTest (5 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 17 tests from 1 test suite ran. (5 ms total) 29: [ PASSED ] 17 tests. 29/81 Test #29: MdrunUtilityUnitTests .......................... Passed 0.49 sec test 30 Start 30: MdrunUtilityMpiUnitTests 30: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdrunutility/tests 30: Test timeout computed to be: 30 30: [==========] Running 13 tests from 2 test suites. 30: [----------] Global test environment set-up. 30: [----------] 6 tests from ThreadAffinityMultiRankTest 30: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 30: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (11 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 30: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (0 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 30: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (0 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 30: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 30: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) 30: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 30: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) 30: [----------] 6 tests from ThreadAffinityMultiRankTest (13 ms total) 30: 30: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (0 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (0 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (0 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (0 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (0 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (0 ms) 30: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 30: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (0 ms) 30: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (3 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 13 tests from 2 test suites ran. (16 ms total) 30: [ PASSED ] 13 tests. 30/81 Test #30: MdrunUtilityMpiUnitTests ....................... Passed 0.49 sec test 31 Start 31: MDSpanTests 31: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MDSpanTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdspan/tests 31: Test timeout computed to be: 30 31: [==========] Running 32 tests from 7 test suites. 31: [----------] Global test environment set-up. 31: [----------] 4 tests from BasicAccessorPolicy 31: [ RUN ] BasicAccessorPolicy.Decay 31: [ OK ] BasicAccessorPolicy.Decay (0 ms) 31: [ RUN ] BasicAccessorPolicy.Access 31: [ OK ] BasicAccessorPolicy.Access (0 ms) 31: [ RUN ] BasicAccessorPolicy.Offset 31: [ OK ] BasicAccessorPolicy.Offset (0 ms) 31: [ RUN ] BasicAccessorPolicy.CopyAccessor 31: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 31: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 31: 31: [----------] 4 tests from ExtentsTest 31: [ RUN ] ExtentsTest.Construction 31: [ OK ] ExtentsTest.Construction (0 ms) 31: [ RUN ] ExtentsTest.PurelyStatic 31: [ OK ] ExtentsTest.PurelyStatic (0 ms) 31: [ RUN ] ExtentsTest.RankNought 31: [ OK ] ExtentsTest.RankNought (0 ms) 31: [ RUN ] ExtentsTest.Assignment 31: [ OK ] ExtentsTest.Assignment (0 ms) 31: [----------] 4 tests from ExtentsTest (0 ms total) 31: 31: [----------] 8 tests from MdSpanExtension 31: [ RUN ] MdSpanExtension.SlicingAllStatic 31: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 31: [ RUN ] MdSpanExtension.SlicingDynamic 31: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 31: [ RUN ] MdSpanExtension.SlicingAllStatic3D 31: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 31: [ RUN ] MdSpanExtension.SlicingEqualsView3D 31: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 31: [ RUN ] MdSpanExtension.additionWorks 31: [ OK ] MdSpanExtension.additionWorks (0 ms) 31: [ RUN ] MdSpanExtension.subtractionWorks 31: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 31: [ RUN ] MdSpanExtension.multiplicationWorks 31: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 31: [ RUN ] MdSpanExtension.divisionWorks 31: [ OK ] MdSpanExtension.divisionWorks (0 ms) 31: [----------] 8 tests from MdSpanExtension (0 ms total) 31: 31: [----------] 3 tests from LayoutTests 31: [ RUN ] LayoutTests.LayoutRightConstruction 31: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 31: [ RUN ] LayoutTests.LayoutRightProperties 31: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 31: [ RUN ] LayoutTests.LayoutRightOperator 31: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 31: [----------] 3 tests from LayoutTests (0 ms total) 31: 31: [----------] 1 test from MdSpanTest 31: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 31: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 31: [----------] 1 test from MdSpanTest (0 ms total) 31: 31: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 31: [ RUN ] MdSpanTest/0.Rank 31: [ OK ] MdSpanTest/0.Rank (0 ms) 31: [ RUN ] MdSpanTest/0.DynamicRank 31: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 31: [ RUN ] MdSpanTest/0.Extents 31: [ OK ] MdSpanTest/0.Extents (0 ms) 31: [ RUN ] MdSpanTest/0.Strides 31: [ OK ] MdSpanTest/0.Strides (0 ms) 31: [ RUN ] MdSpanTest/0.Properties 31: [ OK ] MdSpanTest/0.Properties (0 ms) 31: [ RUN ] MdSpanTest/0.Operator 31: [ OK ] MdSpanTest/0.Operator (0 ms) 31: [----------] 6 tests from MdSpanTest/0 (0 ms total) 31: 31: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 31: [ RUN ] MdSpanTest/1.Rank 31: [ OK ] MdSpanTest/1.Rank (0 ms) 31: [ RUN ] MdSpanTest/1.DynamicRank 31: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 31: [ RUN ] MdSpanTest/1.Extents 31: [ OK ] MdSpanTest/1.Extents (0 ms) 31: [ RUN ] MdSpanTest/1.Strides 31: [ OK ] MdSpanTest/1.Strides (0 ms) 31: [ RUN ] MdSpanTest/1.Properties 31: [ OK ] MdSpanTest/1.Properties (0 ms) 31: [ RUN ] MdSpanTest/1.Operator 31: [ OK ] MdSpanTest/1.Operator (0 ms) 31: [----------] 6 tests from MdSpanTest/1 (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 32 tests from 7 test suites ran. (0 ms total) 31: [ PASSED ] 32 tests. 31/81 Test #31: MDSpanTests .................................... Passed 0.47 sec test 32 Start 32: MdtypesUnitTest 32: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdtypesUnitTest.xml" 32: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/mdtypes/tests 32: Test timeout computed to be: 30 32: [==========] Running 93 tests from 6 test suites. 32: [----------] Global test environment set-up. 32: [----------] 4 tests from ObservablesReducerTest 32: [ RUN ] ObservablesReducerTest.CanMoveAssign 32: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 32: [ RUN ] ObservablesReducerTest.CanMoveConstruct 32: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 32: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 32: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 32: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 32: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 32: [----------] 4 tests from ObservablesReducerTest (0 ms total) 32: 32: [----------] 2 tests from CheckpointDataTest 32: [ RUN ] CheckpointDataTest.SingleDataTest 32: [ OK ] CheckpointDataTest.SingleDataTest (0 ms) 32: [ RUN ] CheckpointDataTest.MultiDataTest 32: [ OK ] CheckpointDataTest.MultiDataTest (5 ms) 32: [----------] 2 tests from CheckpointDataTest (6 ms total) 32: 32: [----------] 7 tests from ForceBuffers 32: [ RUN ] ForceBuffers.ConstructsUnpinned 32: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 32: [ RUN ] ForceBuffers.ConstructsPinned 32: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 32: [ RUN ] ForceBuffers.ConstructsEmpty 32: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 32: [ RUN ] ForceBuffers.ResizeWorks 32: [ OK ] ForceBuffers.ResizeWorks (0 ms) 32: [ RUN ] ForceBuffers.PaddingWorks 32: [ OK ] ForceBuffers.PaddingWorks (0 ms) 32: [ RUN ] ForceBuffers.CopyWorks 32: [ OK ] ForceBuffers.CopyWorks (0 ms) 32: [ RUN ] ForceBuffers.CopyDoesNotPin 32: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 32: [----------] 7 tests from ForceBuffers (0 ms total) 32: 32: [----------] 5 tests from MultipleTimeStepping 32: [ RUN ] MultipleTimeStepping.ChecksNumLevels 32: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 32: [ RUN ] MultipleTimeStepping.SelectsForceGroups 32: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 32: [ RUN ] MultipleTimeStepping.ChecksStepFactor 32: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 32: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 32: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 32: [ RUN ] MultipleTimeStepping.ChecksIntegrator 32: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 32: [----------] 5 tests from MultipleTimeStepping (0 ms total) 32: 32: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 32: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 32: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 32: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (3 ms total) 32: 32: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 32: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 32: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 32: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 93 tests from 6 test suites ran. (10 ms total) 32: [ PASSED ] 93 tests. 32/81 Test #32: MdtypesUnitTest ................................ Passed 0.48 sec test 33 Start 33: OnlineHelpUnitTests 33: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/OnlineHelpUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/onlinehelp/tests 33: Test timeout computed to be: 30 33: [==========] Running 22 tests from 4 test suites. 33: [----------] Global test environment set-up. 33: [----------] 6 tests from TextTableFormatterTest 33: [ RUN ] TextTableFormatterTest.HandlesBasicCase 33: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 33: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 33: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 33: [ RUN ] TextTableFormatterTest.HandlesIndentation 33: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 33: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 33: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 33: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 33: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 33: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 33: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 33: [----------] 6 tests from TextTableFormatterTest (0 ms total) 33: 33: [----------] 3 tests from HelpManagerTest 33: [ RUN ] HelpManagerTest.HandlesRootTopic 33: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 33: [ RUN ] HelpManagerTest.HandlesSubTopics 33: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 33: [ RUN ] HelpManagerTest.HandlesInvalidTopics 33: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 33: [----------] 3 tests from HelpManagerTest (0 ms total) 33: 33: [----------] 2 tests from HelpTopicFormattingTest 33: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 33: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 33: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 33: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 33: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 33: 33: [----------] 11 tests from HelpWriterContextTest 33: [ RUN ] HelpWriterContextTest.FormatsParagraphs 33: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 33: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 33: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 33: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsLiteralText 33: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 33: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 33: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsBulletList 33: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 33: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 33: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsGridTable 33: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 33: [ RUN ] HelpWriterContextTest.FormatsTitles 33: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 33: [----------] 11 tests from HelpWriterContextTest (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 22 tests from 4 test suites ran. (2 ms total) 33: [ PASSED ] 22 tests. 33/81 Test #33: OnlineHelpUnitTests ............................ Passed 0.46 sec test 34 Start 34: OptionsUnitTests 34: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/OptionsUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/options/tests 34: Test timeout computed to be: 30 34: [==========] Running 111 tests from 18 test suites. 34: [----------] Global test environment set-up. 34: [----------] 5 tests from AbstractOptionStorageTest 34: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 34: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 34: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 34: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 34: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 34: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 34: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 34: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 34: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 34: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 34: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 34: 34: [----------] 10 tests from FileNameOptionTest 34: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 34: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 34: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 34: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 34: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 34: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 34: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 34: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 34: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 34: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 34: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 34: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 34: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 34: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 34: [----------] 10 tests from FileNameOptionTest (0 ms total) 34: 34: [----------] 15 tests from FileNameOptionManagerTest 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 34: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 34: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 34: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 34: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 34: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 34: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 34: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 34: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 34: [----------] 15 tests from FileNameOptionManagerTest (0 ms total) 34: 34: [----------] 1 test from OptionsTest 34: [ RUN ] OptionsTest.FailsOnNonsafeStorage 34: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 34: [----------] 1 test from OptionsTest (0 ms total) 34: 34: [----------] 9 tests from OptionsAssignerTest 34: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 34: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 34: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 34: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 34: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesMissingValue 34: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesExtraValue 34: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesGroups 34: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesSections 34: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 34: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 34: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 34: [----------] 9 tests from OptionsAssignerTest (0 ms total) 34: 34: [----------] 4 tests from OptionsAssignerBooleanTest 34: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 34: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 34: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 34: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 34: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 34: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 34: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 34: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 34: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 34: 34: [----------] 13 tests from OptionsAssignerIntegerTest 34: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 34: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 34: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 34: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 34: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 34: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 34: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 34: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 34: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 34: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 34: 34: [----------] 5 tests from OptionsAssignerDoubleTest 34: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 34: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 34: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 34: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 34: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 34: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 34: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 34: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 34: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 34: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 34: 34: [----------] 9 tests from OptionsAssignerStringTest 34: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 34: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 34: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 34: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 34: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 34: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 34: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 34: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 34: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 34: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 34: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 34: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 34: 34: [----------] 6 tests from OptionsAssignerEnumTest 34: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 34: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 34: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 34: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 34: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 34: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 34: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 34: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 34: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 34: 34: [----------] 8 tests from RepeatingOptionSectionTest 34: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 34: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 34: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 34: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 34: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 34: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 34: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 34: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 34: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 34: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 34: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 34: 34: [----------] 1 test from TimeUnitManagerTest 34: [ RUN ] TimeUnitManagerTest.BasicOperations 34: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 34: [----------] 1 test from TimeUnitManagerTest (0 ms total) 34: 34: [----------] 4 tests from TimeUnitBehaviorTest 34: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 34: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 34: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 34: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 34: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 34: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 34: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 34: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 34: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 34: 34: [----------] 2 tests from TreeValueSupportAssignTest 34: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 34: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 34: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 34: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 34: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 34: 34: [----------] 1 test from TreeValueSupportAssignErrorTest 34: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 34: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 34: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 34: 34: [----------] 5 tests from TreeValueSupportCheckTest 34: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 34: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 34: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 34: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 34: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 34: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 34: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 34: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 34: 34: [----------] 6 tests from TreeValueSupportAdjustTest 34: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 34: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 34: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 34: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 34: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 34: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 34: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 34: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 34: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 34: 34: [----------] 7 tests from TreeValueSupportTest 34: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 34: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 34: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsInt64Option 34: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsStringOption 34: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsFloatOption 34: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 34: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 34: [ RUN ] TreeValueSupportTest.SupportsEnumOption 34: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 34: [----------] 7 tests from TreeValueSupportTest (0 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 111 tests from 18 test suites ran. (5 ms total) 34: [ PASSED ] 111 tests. 34/81 Test #34: OptionsUnitTests ............................... Passed 0.47 sec test 35 Start 35: PbcutilUnitTest 35: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/PbcutilUnitTest.xml" 35: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pbcutil/tests 35: Test timeout computed to be: 30 35: [==========] Running 33 tests from 5 test suites. 35: [----------] Global test environment set-up. 35: [----------] 1 test from ShiftTest 35: [ RUN ] ShiftTest.CoordinateShiftWorks 35: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 35: [----------] 1 test from ShiftTest (0 ms total) 35: 35: [----------] 2 tests from MShift 35: [ RUN ] MShift.shiftsAndUnshifts 35: [ OK ] MShift.shiftsAndUnshifts (0 ms) 35: [ RUN ] MShift.shiftsAndUnshiftsSelf 35: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 35: [----------] 2 tests from MShift (0 ms total) 35: 35: [----------] 1 test from PbcTest 35: [ RUN ] PbcTest.CalcShiftsWorks 35: [ OK ] PbcTest.CalcShiftsWorks (1 ms) 35: [----------] 1 test from PbcTest (1 ms total) 35: 35: [----------] 2 tests from PbcEnumsTest 35: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 35: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 35: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 35: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 35: [----------] 2 tests from PbcEnumsTest (0 ms total) 35: 35: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 35: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 35: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 35: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (6 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 33 tests from 5 test suites ran. (8 ms total) 35: [ PASSED ] 33 tests. 35/81 Test #35: PbcutilUnitTest ................................ Passed 0.49 sec test 36 Start 36: RandomUnitTests 36: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/RandomUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/random/tests 36: Test timeout computed to be: 30 36: [==========] Running 44 tests from 10 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from ExponentialDistributionTest 36: [ RUN ] ExponentialDistributionTest.Output 36: [ OK ] ExponentialDistributionTest.Output (0 ms) 36: [ RUN ] ExponentialDistributionTest.Logical 36: [ OK ] ExponentialDistributionTest.Logical (0 ms) 36: [ RUN ] ExponentialDistributionTest.Reset 36: [ OK ] ExponentialDistributionTest.Reset (0 ms) 36: [ RUN ] ExponentialDistributionTest.AltParam 36: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 36: 36: [----------] 4 tests from GammaDistributionTest 36: [ RUN ] GammaDistributionTest.Output 36: [ OK ] GammaDistributionTest.Output (0 ms) 36: [ RUN ] GammaDistributionTest.Logical 36: [ OK ] GammaDistributionTest.Logical (0 ms) 36: [ RUN ] GammaDistributionTest.Reset 36: [ OK ] GammaDistributionTest.Reset (0 ms) 36: [ RUN ] GammaDistributionTest.AltParam 36: [ OK ] GammaDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from GammaDistributionTest (0 ms total) 36: 36: [----------] 4 tests from NormalDistributionTest 36: [ RUN ] NormalDistributionTest.Output 36: [ OK ] NormalDistributionTest.Output (0 ms) 36: [ RUN ] NormalDistributionTest.Logical 36: [ OK ] NormalDistributionTest.Logical (0 ms) 36: [ RUN ] NormalDistributionTest.Reset 36: [ OK ] NormalDistributionTest.Reset (0 ms) 36: [ RUN ] NormalDistributionTest.AltParam 36: [ OK ] NormalDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from NormalDistributionTest (0 ms total) 36: 36: [----------] 1 test from SeedTest 36: [ RUN ] SeedTest.makeRandomSeed 36: [ OK ] SeedTest.makeRandomSeed (0 ms) 36: [----------] 1 test from SeedTest (0 ms total) 36: 36: [----------] 6 tests from TabulatedNormalDistributionTest 36: [ RUN ] TabulatedNormalDistributionTest.Output14 36: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.Output16 36: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 36: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.Logical 36: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.Reset 36: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 36: [ RUN ] TabulatedNormalDistributionTest.AltParam 36: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 36: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 36: 36: [----------] 1 test from TabulatedNormalDistributionTableTest 36: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 36: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (1 ms) 36: [----------] 1 test from TabulatedNormalDistributionTableTest (1 ms total) 36: 36: [----------] 6 tests from ThreeFry2x64Test 36: [ RUN ] ThreeFry2x64Test.Logical 36: [ OK ] ThreeFry2x64Test.Logical (0 ms) 36: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 36: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 36: [ RUN ] ThreeFry2x64Test.Reseed 36: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 36: [ RUN ] ThreeFry2x64Test.Discard 36: [ OK ] ThreeFry2x64Test.Discard (0 ms) 36: [ RUN ] ThreeFry2x64Test.InvalidCounter 36: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 36: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 36: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 36: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 36: 36: [----------] 4 tests from UniformIntDistributionTest 36: [ RUN ] UniformIntDistributionTest.Output 36: [ OK ] UniformIntDistributionTest.Output (0 ms) 36: [ RUN ] UniformIntDistributionTest.Logical 36: [ OK ] UniformIntDistributionTest.Logical (0 ms) 36: [ RUN ] UniformIntDistributionTest.Reset 36: [ OK ] UniformIntDistributionTest.Reset (0 ms) 36: [ RUN ] UniformIntDistributionTest.AltParam 36: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 36: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 36: 36: [----------] 5 tests from UniformRealDistributionTest 36: [ RUN ] UniformRealDistributionTest.GenerateCanonical 36: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 36: [ RUN ] UniformRealDistributionTest.Output 36: [ OK ] UniformRealDistributionTest.Output (0 ms) 36: [ RUN ] UniformRealDistributionTest.Logical 36: [ OK ] UniformRealDistributionTest.Logical (0 ms) 36: [ RUN ] UniformRealDistributionTest.Reset 36: [ OK ] UniformRealDistributionTest.Reset (0 ms) 36: [ RUN ] UniformRealDistributionTest.AltParam 36: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 36: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 36: 36: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 36: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 36: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 36: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 44 tests from 10 test suites ran. (3 ms total) 36: [ PASSED ] 44 tests. 36/81 Test #36: RandomUnitTests ................................ Passed 0.50 sec test 37 Start 37: RestraintTests 37: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/RestraintTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/restraint/tests 37: Test timeout computed to be: 30 37: [==========] Running 1 test from 1 test suite. 37: [----------] Global test environment set-up. 37: [----------] 1 test from RestraintManager 37: [ RUN ] RestraintManager.restraintList 37: [ OK ] RestraintManager.restraintList (0 ms) 37: [----------] 1 test from RestraintManager (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 1 test from 1 test suite ran. (0 ms total) 37: [ PASSED ] 1 test. 37/81 Test #37: RestraintTests ................................. Passed 0.48 sec test 38 Start 38: TableUnitTests 38: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/TableUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tables/tests 38: Test timeout computed to be: 30 38: [==========] Running 20 tests from 2 test suites. 38: [----------] Global test environment set-up. 38: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 38: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 38: [ OK ] SplineTableTest/0.HandlesIncorrectInput (1 ms) 38: [ RUN ] SplineTableTest/0.Sinc 38: [ OK ] SplineTableTest/0.Sinc (0 ms) 38: [ RUN ] SplineTableTest/0.LJ12 38: [ OK ] SplineTableTest/0.LJ12 (15 ms) 38: [ RUN ] SplineTableTest/0.PmeCorrection 38: [ OK ] SplineTableTest/0.PmeCorrection (1 ms) 38: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 38: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 38: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 38: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 38: [ RUN ] SplineTableTest/0.TwoFunctions 38: [ OK ] SplineTableTest/0.TwoFunctions (26 ms) 38: [ RUN ] SplineTableTest/0.ThreeFunctions 38: [ OK ] SplineTableTest/0.ThreeFunctions (29 ms) 38: [ RUN ] SplineTableTest/0.Simd 38: [ OK ] SplineTableTest/0.Simd (6 ms) 38: [ RUN ] SplineTableTest/0.SimdTwoFunctions 38: [ OK ] SplineTableTest/0.SimdTwoFunctions (23 ms) 38: [----------] 10 tests from SplineTableTest/0 (105 ms total) 38: 38: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 38: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 38: [ OK ] SplineTableTest/1.HandlesIncorrectInput (1 ms) 38: [ RUN ] SplineTableTest/1.Sinc 38: [ OK ] SplineTableTest/1.Sinc (0 ms) 38: [ RUN ] SplineTableTest/1.LJ12 38: [ OK ] SplineTableTest/1.LJ12 (1 ms) 38: [ RUN ] SplineTableTest/1.PmeCorrection 38: [ OK ] SplineTableTest/1.PmeCorrection (1 ms) 38: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 38: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 38: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 38: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 38: [ RUN ] SplineTableTest/1.TwoFunctions 38: [ OK ] SplineTableTest/1.TwoFunctions (3 ms) 38: [ RUN ] SplineTableTest/1.ThreeFunctions 38: [ OK ] SplineTableTest/1.ThreeFunctions (4 ms) 38: [ RUN ] SplineTableTest/1.Simd 38: [ OK ] SplineTableTest/1.Simd (1 ms) 38: [ RUN ] SplineTableTest/1.SimdTwoFunctions 38: [ OK ] SplineTableTest/1.SimdTwoFunctions (3 ms) 38: [----------] 10 tests from SplineTableTest/1 (18 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 20 tests from 2 test suites ran. (123 ms total) 38: [ PASSED ] 20 tests. 38/81 Test #38: TableUnitTests ................................. Passed 0.61 sec test 39 Start 39: TaskAssignmentUnitTests 39: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/TaskAssignmentUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/taskassignment/tests 39: Test timeout computed to be: 30 39: [==========] Running 3 tests from 2 test suites. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 39: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 39: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 39: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 39: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 39: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 39: 39: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 39: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 39: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 39: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 3 tests from 2 test suites ran. (0 ms total) 39: [ PASSED ] 3 tests. 39/81 Test #39: TaskAssignmentUnitTests ........................ Passed 0.52 sec test 40 Start 40: GmxTimingTests 40: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/GmxTimingTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/timing/tests 40: Test timeout computed to be: 30 40: [==========] Running 6 tests from 1 test suite. 40: [----------] Global test environment set-up. 40: [----------] 6 tests from TimingTest 40: [ RUN ] TimingTest.ElementCountingWorks 40: [ OK ] TimingTest.ElementCountingWorks (0 ms) 40: [ RUN ] TimingTest.ElementNoCountingWorks 40: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 40: [ RUN ] TimingTest.SubElementCountingWorks 40: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 40: [ RUN ] TimingTest.SubElementNoCountingWorks 40: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 40: [ RUN ] TimingTest.RunWallCycle 40: [ OK ] TimingTest.RunWallCycle (1 ms) 40: [ RUN ] TimingTest.RunWallCycleSub 40: [ OK ] TimingTest.RunWallCycleSub (0 ms) 40: [----------] 6 tests from TimingTest (1 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 6 tests from 1 test suite ran. (1 ms total) 40: [ PASSED ] 6 tests. 40/81 Test #40: GmxTimingTests ................................. Passed 0.50 sec test 41 Start 41: TopologyTest 41: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/TopologyTest.xml" 41: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/topology/tests 41: Test timeout computed to be: 30 41: [==========] Running 40 tests from 7 test suites. 41: [----------] Global test environment set-up. 41: [----------] 3 tests from ExclusionBlockTest 41: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 41: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 41: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 41: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 41: [ RUN ] ExclusionBlockTest.MergeExclusions 41: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 41: [----------] 3 tests from ExclusionBlockTest (0 ms total) 41: 41: [----------] 6 tests from InteractionListTest 41: [ RUN ] InteractionListTest.EmptyWorks 41: [ OK ] InteractionListTest.EmptyWorks (0 ms) 41: [ RUN ] InteractionListTest.CanAddInteractionArray 41: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 41: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 41: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 41: [ RUN ] InteractionListTest.CanAddInteractionPointer 41: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 41: [ RUN ] InteractionListTest.CanAddListToOtherList 41: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 41: [ RUN ] InteractionListTest.ClearingWorks 41: [ OK ] InteractionListTest.ClearingWorks (0 ms) 41: [----------] 6 tests from InteractionListTest (0 ms total) 41: 41: [----------] 5 tests from MtopTest 41: [ RUN ] MtopTest.RangeBasedLoop 41: [ OK ] MtopTest.RangeBasedLoop (0 ms) 41: [ RUN ] MtopTest.Operators 41: [ OK ] MtopTest.Operators (0 ms) 41: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 41: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 41: [ RUN ] MtopTest.AtomHasPerturbedChargeIn14Interaction 41: [ OK ] MtopTest.AtomHasPerturbedChargeIn14Interaction (0 ms) 41: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 41: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 41: [----------] 5 tests from MtopTest (0 ms total) 41: 41: [----------] 2 tests from IListRangeTest 41: [ RUN ] IListRangeTest.RangeBasedLoopWorks 41: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 41: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 41: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 41: [----------] 2 tests from IListRangeTest (0 ms total) 41: 41: [----------] 13 tests from StringTableTest 41: [ RUN ] StringTableTest.AddSingleEntry 41: [ OK ] StringTableTest.AddSingleEntry (0 ms) 41: [ RUN ] StringTableTest.CanAccessWithAt 41: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 41: [ RUN ] StringTableTest.CanAccessWithBracket 41: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 41: [ RUN ] StringTableTest.ThrowsOutOfRange 41: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 41: [ RUN ] StringTableTest.StringCompareIsCorrect 41: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 41: [ RUN ] StringTableTest.AddTwoDistinctEntries 41: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 41: [ RUN ] StringTableTest.TryToAddDuplicates 41: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 41: [ RUN ] StringTableTest.AddLargeNumberOfEntries 41: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 41: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 41: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 41: [ RUN ] StringTableTest.CanWriteToBuffer 41: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 41: [ RUN ] StringTableTest.Roundtrip 41: [ OK ] StringTableTest.Roundtrip (0 ms) 41: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 41: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 41: [ RUN ] StringTableTest.CanCopyToLegacyTable 41: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 41: [----------] 13 tests from StringTableTest (1 ms total) 41: 41: [----------] 6 tests from LegacySymtabTest 41: [ RUN ] LegacySymtabTest.EmptyOnOpen 41: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 41: [ RUN ] LegacySymtabTest.AddSingleEntry 41: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 41: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 41: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 41: [ RUN ] LegacySymtabTest.TryToAddDuplicates 41: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 41: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 41: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 41: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 41: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 41: [----------] 6 tests from LegacySymtabTest (0 ms total) 41: 41: [----------] 5 tests from TopSortTest 41: [ RUN ] TopSortTest.WorksOnEmptyIdef 41: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 41: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 41: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 41: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 41: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 41: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 41: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 41: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 41: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 41: [----------] 5 tests from TopSortTest (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 40 tests from 7 test suites ran. (2 ms total) 41: [ PASSED ] 40 tests. 41/81 Test #41: TopologyTest ................................... Passed 0.51 sec test 42 Start 42: PullTest 42: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/PullTest.xml" 42: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/pulling/tests 42: Test timeout computed to be: 30 42: [==========] Running 8 tests from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 8 tests from PullTest 42: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 42: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 42: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 42: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 42: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 42: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 42: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 42: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 42: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 42: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 42: [ RUN ] PullTest.TransformationCoordSimple 42: [ OK ] PullTest.TransformationCoordSimple (0 ms) 42: [ RUN ] PullTest.TransformationCoordAdvanced 42: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 42: [ RUN ] PullTest.TransformationCoordDummyExpression 42: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 42: [----------] 8 tests from PullTest (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 8 tests from 1 test suite ran. (0 ms total) 42: [ PASSED ] 8 tests. 42/81 Test #42: PullTest ....................................... Passed 0.49 sec test 43 Start 43: SimdUnitTests 43: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/SimdUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/simd/tests 43: Test timeout computed to be: 30 43: [==========] Running 288 tests from 22 test suites. 43: [----------] Global test environment set-up. 43: [----------] 9 tests from SimdBootstrapTest 43: [ RUN ] SimdBootstrapTest.loadStore 43: [ OK ] SimdBootstrapTest.loadStore (0 ms) 43: [ RUN ] SimdBootstrapTest.loadU 43: [ OK ] SimdBootstrapTest.loadU (0 ms) 43: [ RUN ] SimdBootstrapTest.storeU 43: [ OK ] SimdBootstrapTest.storeU (0 ms) 43: [ RUN ] SimdBootstrapTest.loadStoreI 43: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 43: [ RUN ] SimdBootstrapTest.loadUI 43: [ OK ] SimdBootstrapTest.loadUI (0 ms) 43: [ RUN ] SimdBootstrapTest.storeUI 43: [ OK ] SimdBootstrapTest.storeUI (0 ms) 43: [ RUN ] SimdBootstrapTest.simd4LoadStore 43: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 43: [ RUN ] SimdBootstrapTest.simd4LoadU 43: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 43: [ RUN ] SimdBootstrapTest.simd4StoreU 43: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 43: [----------] 9 tests from SimdBootstrapTest (0 ms total) 43: 43: [----------] 41 tests from SimdScalarTest 43: [ RUN ] SimdScalarTest.load 43: [ OK ] SimdScalarTest.load (0 ms) 43: [ RUN ] SimdScalarTest.loadU 43: [ OK ] SimdScalarTest.loadU (0 ms) 43: [ RUN ] SimdScalarTest.store 43: [ OK ] SimdScalarTest.store (0 ms) 43: [ RUN ] SimdScalarTest.storeU 43: [ OK ] SimdScalarTest.storeU (0 ms) 43: [ RUN ] SimdScalarTest.setZero 43: [ OK ] SimdScalarTest.setZero (0 ms) 43: [ RUN ] SimdScalarTest.andNot 43: [ OK ] SimdScalarTest.andNot (0 ms) 43: [ RUN ] SimdScalarTest.fma 43: [ OK ] SimdScalarTest.fma (0 ms) 43: [ RUN ] SimdScalarTest.fms 43: [ OK ] SimdScalarTest.fms (0 ms) 43: [ RUN ] SimdScalarTest.fnma 43: [ OK ] SimdScalarTest.fnma (0 ms) 43: [ RUN ] SimdScalarTest.fnms 43: [ OK ] SimdScalarTest.fnms (0 ms) 43: [ RUN ] SimdScalarTest.maskAdd 43: [ OK ] SimdScalarTest.maskAdd (0 ms) 43: [ RUN ] SimdScalarTest.maskzMul 43: [ OK ] SimdScalarTest.maskzMul (0 ms) 43: [ RUN ] SimdScalarTest.maskzFma 43: [ OK ] SimdScalarTest.maskzFma (0 ms) 43: [ RUN ] SimdScalarTest.abs 43: [ OK ] SimdScalarTest.abs (0 ms) 43: [ RUN ] SimdScalarTest.max 43: [ OK ] SimdScalarTest.max (0 ms) 43: [ RUN ] SimdScalarTest.min 43: [ OK ] SimdScalarTest.min (0 ms) 43: [ RUN ] SimdScalarTest.round 43: [ OK ] SimdScalarTest.round (0 ms) 43: [ RUN ] SimdScalarTest.trunc 43: [ OK ] SimdScalarTest.trunc (0 ms) 43: [ RUN ] SimdScalarTest.reduce 43: [ OK ] SimdScalarTest.reduce (0 ms) 43: [ RUN ] SimdScalarTest.testBits 43: [ OK ] SimdScalarTest.testBits (0 ms) 43: [ RUN ] SimdScalarTest.anyTrue 43: [ OK ] SimdScalarTest.anyTrue (0 ms) 43: [ RUN ] SimdScalarTest.selectByMask 43: [ OK ] SimdScalarTest.selectByMask (0 ms) 43: [ RUN ] SimdScalarTest.selectByNotMask 43: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 43: [ RUN ] SimdScalarTest.blend 43: [ OK ] SimdScalarTest.blend (0 ms) 43: [ RUN ] SimdScalarTest.cvtR2I 43: [ OK ] SimdScalarTest.cvtR2I (0 ms) 43: [ RUN ] SimdScalarTest.cvttR2I 43: [ OK ] SimdScalarTest.cvttR2I (0 ms) 43: [ RUN ] SimdScalarTest.cvtI2R 43: [ OK ] SimdScalarTest.cvtI2R (0 ms) 43: [ RUN ] SimdScalarTest.cvtF2D 43: [ OK ] SimdScalarTest.cvtF2D (0 ms) 43: [ RUN ] SimdScalarTest.cvtD2D 43: [ OK ] SimdScalarTest.cvtD2D (0 ms) 43: [ RUN ] SimdScalarTest.loadI 43: [ OK ] SimdScalarTest.loadI (0 ms) 43: [ RUN ] SimdScalarTest.loadUI 43: [ OK ] SimdScalarTest.loadUI (0 ms) 43: [ RUN ] SimdScalarTest.storeI 43: [ OK ] SimdScalarTest.storeI (0 ms) 43: [ RUN ] SimdScalarTest.storeUI 43: [ OK ] SimdScalarTest.storeUI (0 ms) 43: [ RUN ] SimdScalarTest.andNotI 43: [ OK ] SimdScalarTest.andNotI (0 ms) 43: [ RUN ] SimdScalarTest.testBitsI 43: [ OK ] SimdScalarTest.testBitsI (0 ms) 43: [ RUN ] SimdScalarTest.selectByMaskI 43: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 43: [ RUN ] SimdScalarTest.selectByNotMaskI 43: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 43: [ RUN ] SimdScalarTest.blendI 43: [ OK ] SimdScalarTest.blendI (0 ms) 43: [ RUN ] SimdScalarTest.cvtB2IB 43: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 43: [ RUN ] SimdScalarTest.cvtIB2B 43: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 43: [ RUN ] SimdScalarTest.expandScalarsToTriplets 43: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 43: [----------] 41 tests from SimdScalarTest (0 ms total) 43: 43: [----------] 8 tests from SimdScalarUtilTest 43: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 43: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 43: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 43: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 43: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 43: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 43: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 43: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 43: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 43: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 43: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 43: 43: [----------] 37 tests from SimdScalarMathTest 43: [ RUN ] SimdScalarMathTest.copysign 43: [ OK ] SimdScalarMathTest.copysign (0 ms) 43: [ RUN ] SimdScalarMathTest.invsqrtPair 43: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 43: [ RUN ] SimdScalarMathTest.inv 43: [ OK ] SimdScalarMathTest.inv (0 ms) 43: [ RUN ] SimdScalarMathTest.maskzInvsqrt 43: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 43: [ RUN ] SimdScalarMathTest.log 43: [ OK ] SimdScalarMathTest.log (0 ms) 43: [ RUN ] SimdScalarMathTest.exp2 43: [ OK ] SimdScalarMathTest.exp2 (0 ms) 43: [ RUN ] SimdScalarMathTest.exp 43: [ OK ] SimdScalarMathTest.exp (0 ms) 43: [ RUN ] SimdScalarMathTest.erf 43: [ OK ] SimdScalarMathTest.erf (0 ms) 43: [ RUN ] SimdScalarMathTest.erfc 43: [ OK ] SimdScalarMathTest.erfc (0 ms) 43: [ RUN ] SimdScalarMathTest.sincos 43: [ OK ] SimdScalarMathTest.sincos (0 ms) 43: [ RUN ] SimdScalarMathTest.sin 43: [ OK ] SimdScalarMathTest.sin (0 ms) 43: [ RUN ] SimdScalarMathTest.cos 43: [ OK ] SimdScalarMathTest.cos (0 ms) 43: [ RUN ] SimdScalarMathTest.tan 43: [ OK ] SimdScalarMathTest.tan (0 ms) 43: [ RUN ] SimdScalarMathTest.asin 43: [ OK ] SimdScalarMathTest.asin (0 ms) 43: [ RUN ] SimdScalarMathTest.acos 43: [ OK ] SimdScalarMathTest.acos (0 ms) 43: [ RUN ] SimdScalarMathTest.atan 43: [ OK ] SimdScalarMathTest.atan (0 ms) 43: [ RUN ] SimdScalarMathTest.atan2 43: [ OK ] SimdScalarMathTest.atan2 (0 ms) 43: [ RUN ] SimdScalarMathTest.pmeForceCorrection 43: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 43: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 43: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 43: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 43: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.invSingleAccuracy 43: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 43: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.logSingleAccuracy 43: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 43: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.expSingleAccuracy 43: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 43: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 43: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 43: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 43: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 43: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 43: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 43: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 43: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 43: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 43: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 43: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 43: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 43: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 43: [----------] 37 tests from SimdScalarMathTest (0 ms total) 43: 43: [----------] 1 test from SimdTest 43: [ RUN ] SimdTest.GmxAligned 43: [ OK ] SimdTest.GmxAligned (0 ms) 43: [----------] 1 test from SimdTest (0 ms total) 43: 43: [----------] 42 tests from SimdFloatingpointTest 43: [ RUN ] SimdFloatingpointTest.setZero 43: [ OK ] SimdFloatingpointTest.setZero (0 ms) 43: [ RUN ] SimdFloatingpointTest.set 43: [ OK ] SimdFloatingpointTest.set (0 ms) 43: [ RUN ] SimdFloatingpointTest.add 43: [ OK ] SimdFloatingpointTest.add (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskAdd 43: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 43: [ RUN ] SimdFloatingpointTest.sub 43: [ OK ] SimdFloatingpointTest.sub (0 ms) 43: [ RUN ] SimdFloatingpointTest.mul 43: [ OK ] SimdFloatingpointTest.mul (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzMul 43: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 43: [ RUN ] SimdFloatingpointTest.fma 43: [ OK ] SimdFloatingpointTest.fma (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzFma 43: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 43: [ RUN ] SimdFloatingpointTest.fms 43: [ OK ] SimdFloatingpointTest.fms (0 ms) 43: [ RUN ] SimdFloatingpointTest.fnma 43: [ OK ] SimdFloatingpointTest.fnma (0 ms) 43: [ RUN ] SimdFloatingpointTest.fnms 43: [ OK ] SimdFloatingpointTest.fnms (0 ms) 43: [ RUN ] SimdFloatingpointTest.abs 43: [ OK ] SimdFloatingpointTest.abs (0 ms) 43: [ RUN ] SimdFloatingpointTest.neg 43: [ OK ] SimdFloatingpointTest.neg (0 ms) 43: [ RUN ] SimdFloatingpointTest.and 43: [ OK ] SimdFloatingpointTest.and (0 ms) 43: [ RUN ] SimdFloatingpointTest.or 43: [ OK ] SimdFloatingpointTest.or (0 ms) 43: [ RUN ] SimdFloatingpointTest.xor 43: [ OK ] SimdFloatingpointTest.xor (0 ms) 43: [ RUN ] SimdFloatingpointTest.andNot 43: [ OK ] SimdFloatingpointTest.andNot (0 ms) 43: [ RUN ] SimdFloatingpointTest.max 43: [ OK ] SimdFloatingpointTest.max (0 ms) 43: [ RUN ] SimdFloatingpointTest.min 43: [ OK ] SimdFloatingpointTest.min (0 ms) 43: [ RUN ] SimdFloatingpointTest.round 43: [ OK ] SimdFloatingpointTest.round (0 ms) 43: [ RUN ] SimdFloatingpointTest.roundMode 43: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 43: [ RUN ] SimdFloatingpointTest.trunc 43: [ OK ] SimdFloatingpointTest.trunc (0 ms) 43: [ RUN ] SimdFloatingpointTest.frexp 43: [ OK ] SimdFloatingpointTest.frexp (0 ms) 43: [ RUN ] SimdFloatingpointTest.ldexp 43: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 43: [ RUN ] SimdFloatingpointTest.rsqrt 43: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzRsqrt 43: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 43: [ RUN ] SimdFloatingpointTest.rcp 43: [ OK ] SimdFloatingpointTest.rcp (0 ms) 43: [ RUN ] SimdFloatingpointTest.maskzRcp 43: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 43: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 43: [ RUN ] SimdFloatingpointTest.selectByNotMask 43: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpNe 43: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpLe 43: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 43: [ RUN ] SimdFloatingpointTest.cmpLt 43: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 43: [ RUN ] SimdFloatingpointTest.testBits 43: [ OK ] SimdFloatingpointTest.testBits (0 ms) 43: [ RUN ] SimdFloatingpointTest.andB 43: [ OK ] SimdFloatingpointTest.andB (0 ms) 43: [ RUN ] SimdFloatingpointTest.orB 43: [ OK ] SimdFloatingpointTest.orB (0 ms) 43: [ RUN ] SimdFloatingpointTest.anyTrueB 43: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 43: [ RUN ] SimdFloatingpointTest.blend 43: [ OK ] SimdFloatingpointTest.blend (0 ms) 43: [ RUN ] SimdFloatingpointTest.reduce 43: [ OK ] SimdFloatingpointTest.reduce (0 ms) 43: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 43: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 43: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 43: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 43: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 43: 43: [----------] 16 tests from SimdFloatingpointUtilTest 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 43: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 43: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 43: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 43: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 43: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 43: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 43: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 43: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 43: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 43: 43: [----------] 23 tests from SimdIntegerTest 43: [ RUN ] SimdIntegerTest.setZero 43: [ OK ] SimdIntegerTest.setZero (0 ms) 43: [ RUN ] SimdIntegerTest.set 43: [ OK ] SimdIntegerTest.set (0 ms) 43: [ RUN ] SimdIntegerTest.add 43: [ OK ] SimdIntegerTest.add (0 ms) 43: [ RUN ] SimdIntegerTest.sub 43: [ OK ] SimdIntegerTest.sub (0 ms) 43: [ RUN ] SimdIntegerTest.mul 43: [ OK ] SimdIntegerTest.mul (0 ms) 43: [ RUN ] SimdIntegerTest.and 43: [ OK ] SimdIntegerTest.and (0 ms) 43: [ RUN ] SimdIntegerTest.andNot 43: [ OK ] SimdIntegerTest.andNot (0 ms) 43: [ RUN ] SimdIntegerTest.or 43: [ OK ] SimdIntegerTest.or (0 ms) 43: [ RUN ] SimdIntegerTest.xor 43: [ OK ] SimdIntegerTest.xor (0 ms) 43: [ RUN ] SimdIntegerTest.extract 43: [ OK ] SimdIntegerTest.extract (0 ms) 43: [ RUN ] SimdIntegerTest.cvtR2I 43: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 43: [ RUN ] SimdIntegerTest.cvttR2I 43: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 43: [ RUN ] SimdIntegerTest.cvtI2R 43: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 43: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 43: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 43: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 43: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 43: [ RUN ] SimdIntegerTest.cmpLt 43: [ OK ] SimdIntegerTest.cmpLt (0 ms) 43: [ RUN ] SimdIntegerTest.testBits 43: [ OK ] SimdIntegerTest.testBits (0 ms) 43: [ RUN ] SimdIntegerTest.andB 43: [ OK ] SimdIntegerTest.andB (0 ms) 43: [ RUN ] SimdIntegerTest.orB 43: [ OK ] SimdIntegerTest.orB (0 ms) 43: [ RUN ] SimdIntegerTest.anyTrue 43: [ OK ] SimdIntegerTest.anyTrue (0 ms) 43: [ RUN ] SimdIntegerTest.blend 43: [ OK ] SimdIntegerTest.blend (0 ms) 43: [ RUN ] SimdIntegerTest.cvtB2IB 43: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 43: [ RUN ] SimdIntegerTest.cvtIB2B 43: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 43: [----------] 23 tests from SimdIntegerTest (0 ms total) 43: 43: [----------] 56 tests from SimdMathTest 43: [ RUN ] SimdMathTest.generateTestPointsFloat 43: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 43: [ RUN ] SimdMathTest.copysign 43: [ OK ] SimdMathTest.copysign (0 ms) 43: [ RUN ] SimdMathTest.invsqrt 43: [ OK ] SimdMathTest.invsqrt (0 ms) 43: [ RUN ] SimdMathTest.maskzInvsqrt 43: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 43: [ RUN ] SimdMathTest.invsqrtPair 43: [ OK ] SimdMathTest.invsqrtPair (0 ms) 43: [ RUN ] SimdMathTest.sqrt 43: [ OK ] SimdMathTest.sqrt (0 ms) 43: [ RUN ] SimdMathTest.sqrtUnsafe 43: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 43: [ RUN ] SimdMathTest.inv 43: [ OK ] SimdMathTest.inv (2 ms) 43: [ RUN ] SimdMathTest.maskzInv 43: [ OK ] SimdMathTest.maskzInv (0 ms) 43: [ RUN ] SimdMathTest.cbrt 43: [ OK ] SimdMathTest.cbrt (0 ms) 43: [ RUN ] SimdMathTest.invcbrt 43: [ OK ] SimdMathTest.invcbrt (3 ms) 43: [ RUN ] SimdMathTest.log2 43: [ OK ] SimdMathTest.log2 (0 ms) 43: [ RUN ] SimdMathTest.log 43: [ OK ] SimdMathTest.log (0 ms) 43: [ RUN ] SimdMathTest.exp2 43: [ OK ] SimdMathTest.exp2 (2 ms) 43: [ RUN ] SimdMathTest.exp2Unsafe 43: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 43: [ RUN ] SimdMathTest.exp 43: [ OK ] SimdMathTest.exp (3 ms) 43: [ RUN ] SimdMathTest.expUnsafe 43: [ OK ] SimdMathTest.expUnsafe (0 ms) 43: [ RUN ] SimdMathTest.pow 43: [ OK ] SimdMathTest.pow (0 ms) 43: [ RUN ] SimdMathTest.powUnsafe 43: [ OK ] SimdMathTest.powUnsafe (0 ms) 43: [ RUN ] SimdMathTest.erf 43: [ OK ] SimdMathTest.erf (1 ms) 43: [ RUN ] SimdMathTest.erfc 43: [ OK ] SimdMathTest.erfc (2 ms) 43: [ RUN ] SimdMathTest.sin 43: [ OK ] SimdMathTest.sin (1 ms) 43: [ RUN ] SimdMathTest.cos 43: [ OK ] SimdMathTest.cos (1 ms) 43: [ RUN ] SimdMathTest.tan 43: [ OK ] SimdMathTest.tan (1 ms) 43: [ RUN ] SimdMathTest.asin 43: [ OK ] SimdMathTest.asin (0 ms) 43: [ RUN ] SimdMathTest.acos 43: [ OK ] SimdMathTest.acos (1 ms) 43: [ RUN ] SimdMathTest.atan 43: [ OK ] SimdMathTest.atan (1 ms) 43: [ RUN ] SimdMathTest.atan2 43: [ OK ] SimdMathTest.atan2 (0 ms) 43: [ RUN ] SimdMathTest.pmeForceCorrection 43: [ OK ] SimdMathTest.pmeForceCorrection (1 ms) 43: [ RUN ] SimdMathTest.pmePotentialCorrection 43: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 43: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 43: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 43: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.sqrtSingleAccuracy 43: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 43: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.invSingleAccuracy 43: [ OK ] SimdMathTest.invSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.cbrtSingleAccuracy 43: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 43: [ OK ] SimdMathTest.invcbrtSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.log2SingleAccuracy 43: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.logSingleAccuracy 43: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.exp2SingleAccuracy 43: [ OK ] SimdMathTest.exp2SingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 43: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.expSingleAccuracy 43: [ OK ] SimdMathTest.expSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 43: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.powSingleAccuracy 43: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 43: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 43: [ RUN ] SimdMathTest.erfSingleAccuracy 43: [ OK ] SimdMathTest.erfSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.erfcSingleAccuracy 43: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.sinSingleAccuracy 43: [ OK ] SimdMathTest.sinSingleAccuracy (2 ms) 43: [ RUN ] SimdMathTest.cosSingleAccuracy 43: [ OK ] SimdMathTest.cosSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.tanSingleAccuracy 43: [ OK ] SimdMathTest.tanSingleAccuracy (1 ms) 43: [ RUN ] SimdMathTest.asinSingleAccuracy 43: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.acosSingleAccuracy 43: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.atanSingleAccuracy 43: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.atan2SingleAccuracy 43: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 43: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 43: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 43: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 43: [----------] 56 tests from SimdMathTest (61 ms total) 43: 43: [----------] 1 test from EmptyArrayRefTest 43: [ RUN ] EmptyArrayRefTest.IsEmpty 43: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 43: [----------] 1 test from EmptyArrayRefTest (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 43: 43: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 43: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 43: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 43: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 43: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 43: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 43: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 43: 43: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefReadWriteTest/0.Assignment 43: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 43: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 43: 43: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefReadWriteTest/1.Assignment 43: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 43: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 43: 43: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefArithmeticTest/0.Basic 43: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 43: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 43: 43: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 43: [ RUN ] ArrayRefArithmeticTest/1.Basic 43: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 43: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 43: 43: [----------] 3 tests from SimdVectorOperationsTest 43: [ RUN ] SimdVectorOperationsTest.iprod 43: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 43: [ RUN ] SimdVectorOperationsTest.norm2 43: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 43: [ RUN ] SimdVectorOperationsTest.cprod 43: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 43: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 43: 43: [----------] 32 tests from Simd4FloatingpointTest 43: [ RUN ] Simd4FloatingpointTest.setZero 43: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 43: [ RUN ] Simd4FloatingpointTest.set 43: [ OK ] Simd4FloatingpointTest.set (0 ms) 43: [ RUN ] Simd4FloatingpointTest.add 43: [ OK ] Simd4FloatingpointTest.add (0 ms) 43: [ RUN ] Simd4FloatingpointTest.sub 43: [ OK ] Simd4FloatingpointTest.sub (0 ms) 43: [ RUN ] Simd4FloatingpointTest.mul 43: [ OK ] Simd4FloatingpointTest.mul (0 ms) 43: [ RUN ] Simd4FloatingpointTest.fma 43: [ OK ] Simd4FloatingpointTest.fma (0 ms) 43: [ RUN ] Simd4FloatingpointTest.fms 43: [ OK ] Simd4FloatingpointTest.fms (0 ms) 43: [ RUN ] Simd4FloatingpointTest.fnma 43: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 43: [ RUN ] Simd4FloatingpointTest.fnms 43: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 43: [ RUN ] Simd4FloatingpointTest.abs 43: [ OK ] Simd4FloatingpointTest.abs (0 ms) 43: [ RUN ] Simd4FloatingpointTest.neg 43: [ OK ] Simd4FloatingpointTest.neg (0 ms) 43: [ RUN ] Simd4FloatingpointTest.and 43: [ OK ] Simd4FloatingpointTest.and (0 ms) 43: [ RUN ] Simd4FloatingpointTest.or 43: [ OK ] Simd4FloatingpointTest.or (0 ms) 43: [ RUN ] Simd4FloatingpointTest.xor 43: [ OK ] Simd4FloatingpointTest.xor (0 ms) 43: [ RUN ] Simd4FloatingpointTest.andNot 43: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 43: [ RUN ] Simd4FloatingpointTest.max 43: [ OK ] Simd4FloatingpointTest.max (0 ms) 43: [ RUN ] Simd4FloatingpointTest.min 43: [ OK ] Simd4FloatingpointTest.min (0 ms) 43: [ RUN ] Simd4FloatingpointTest.round 43: [ OK ] Simd4FloatingpointTest.round (0 ms) 43: [ RUN ] Simd4FloatingpointTest.trunc 43: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 43: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 43: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 43: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 43: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 43: [ RUN ] Simd4FloatingpointTest.selectByNotMask 43: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 43: [ RUN ] Simd4FloatingpointTest.cmpNe 43: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 43: [ RUN ] Simd4FloatingpointTest.cmpLe 43: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 43: [ RUN ] Simd4FloatingpointTest.cmpLt 43: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 43: [ RUN ] Simd4FloatingpointTest.andB 43: [ OK ] Simd4FloatingpointTest.andB (0 ms) 43: [ RUN ] Simd4FloatingpointTest.orB 43: [ OK ] Simd4FloatingpointTest.orB (0 ms) 43: [ RUN ] Simd4FloatingpointTest.anyTrue 43: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 43: [ RUN ] Simd4FloatingpointTest.blend 43: [ OK ] Simd4FloatingpointTest.blend (0 ms) 43: [ RUN ] Simd4FloatingpointTest.reduce 43: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 43: [ RUN ] Simd4FloatingpointTest.dotProduct 43: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 43: [ RUN ] Simd4FloatingpointTest.transpose 43: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 43: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 43: 43: [----------] 2 tests from Simd4MathTest 43: [ RUN ] Simd4MathTest.invsqrt 43: [ OK ] Simd4MathTest.invsqrt (0 ms) 43: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 43: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 43: [----------] 2 tests from Simd4MathTest (0 ms total) 43: 43: [----------] 1 test from Simd4VectorOperationsTest 43: [ RUN ] Simd4VectorOperationsTest.norm2 43: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 43: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 288 tests from 22 test suites ran. (64 ms total) 43: [ PASSED ] 288 tests. 43/81 Test #43: SimdUnitTests .................................. Passed 0.57 sec test 44 Start 44: CompatibilityHelpersTests 44: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/CompatibilityHelpersTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/compat/tests 44: Test timeout computed to be: 30 44: [==========] Running 9 tests from 6 test suites. 44: [----------] Global test environment set-up. 44: [----------] 4 tests from TemplateMPTest 44: [ RUN ] TemplateMPTest.MpWithIndexInt 44: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 44: [ RUN ] TemplateMPTest.MpWithIndexIntBad 44: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 44: [ RUN ] TemplateMPTest.MpWithIndexBool 44: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 44: [ RUN ] TemplateMPTest.MpWithIndexEnum 44: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 44: [----------] 4 tests from TemplateMPTest (0 ms total) 44: 44: [----------] 1 test from NotNullConstruction 44: [ RUN ] NotNullConstruction.Works 44: [ OK ] NotNullConstruction.Works (0 ms) 44: [----------] 1 test from NotNullConstruction (0 ms total) 44: 44: [----------] 1 test from NotNullCasting 44: [ RUN ] NotNullCasting.Works 44: [ OK ] NotNullCasting.Works (0 ms) 44: [----------] 1 test from NotNullCasting (0 ms total) 44: 44: [----------] 1 test from NotNullAssignment 44: [ RUN ] NotNullAssignment.Works 44: [ OK ] NotNullAssignment.Works (0 ms) 44: [----------] 1 test from NotNullAssignment (0 ms total) 44: 44: [----------] 1 test from MakeNotNull 44: [ RUN ] MakeNotNull.Works 44: [ OK ] MakeNotNull.Works (0 ms) 44: [----------] 1 test from MakeNotNull (0 ms total) 44: 44: [----------] 1 test from NotNull 44: [ RUN ] NotNull.WorksInContainers 44: [ OK ] NotNull.WorksInContainers (0 ms) 44: [----------] 1 test from NotNull (0 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 9 tests from 6 test suites ran. (0 ms total) 44: [ PASSED ] 9 tests. 44/81 Test #44: CompatibilityHelpersTests ...................... Passed 0.48 sec test 45 Start 45: GmxAnaTest 45: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/GmxAnaTest.xml" 45: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxana/tests 45: Test timeout computed to be: 600 45: [==========] Running 22 tests from 4 test suites. 45: [----------] Global test environment set-up. 45: [----------] 5 tests from Entropy 45: [ RUN ] Entropy.Schlitter_300_NoLinear 45: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 45: [ RUN ] Entropy.Schlitter_300_Linear 45: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 45: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 45: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 45: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 45: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 45: [ RUN ] Entropy.QuasiHarmonic_200_Linear 45: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 45: [----------] 5 tests from Entropy (0 ms total) 45: 45: [----------] 1 test from GmxChiTest 45: [ RUN ] GmxChiTest.gmxchiWorksWithAll 45: 45: 10 residues with dihedrals found 45: 46 dihedrals found 45: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 45: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 45: j after resetting (nr. active dihedrals) = 46 45: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 45: Now calculating transitions... 45: Total number of transitions: 0 45: Now printing out transitions and OPs... 45: Now printing out rotamer occupancies... 45: Now calculating Chi product trajectories... 45: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 45: 45: gmx chi is deprecated. 45: See https://gitlab.com/gromacs/gromacs/-/issues/4108 if 45: you are interested in preserving it! 45: [ OK ] GmxChiTest.gmxchiWorksWithAll (994 ms) 45: [----------] 1 test from GmxChiTest (1123 ms total) 45: 45: [----------] 10 tests from MindistTest 45: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.mindistWorksWithSingleAtoms (16 ms) 45: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 2: 'atom3' 45: Selected 3: 'atoms12' 45: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 45: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 45: [ RUN ] MindistTest.mindistPicksUpContacts 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 45: [ RUN ] MindistTest.ngWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: Selected 2: 'atom3' 45: [ OK ] MindistTest.ngWorks (0 ms) 45: [ RUN ] MindistTest.groupWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 3: 'atoms12' 45: Selected 2: 'atom3' 45: [ OK ] MindistTest.groupWorks (0 ms) 45: [ RUN ] MindistTest.maxDistWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 2: 'atom3' 45: Selected 3: 'atoms12' 45: [ OK ] MindistTest.maxDistWorks (0 ms) 45: [ RUN ] MindistTest.noPbcWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 0: 'atom1' 45: Selected 1: 'atom2' 45: [ OK ] MindistTest.noPbcWorks (0 ms) 45: [ RUN ] MindistTest.resPerTimeWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 3: 'atoms12' 45: Selected 2: 'atom3' 45: [ OK ] MindistTest.resPerTimeWorks (0 ms) 45: [ RUN ] MindistTest.matrixWorks 45: Group 0 ( atom1) has 1 elements 45: Group 1 ( atom2) has 1 elements 45: Group 2 ( atom3) has 1 elements 45: Group 3 ( atoms12) has 2 elements 45: Group 4 ( atoms23) has 2 elements 45: Group 5 ( atoms123) has 3 elements 45: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 45: Reading frame 0 time 0.000 Last frame 0 time 0.000 45: Selected 5: 'atoms123' 45: Special case: making distance matrix between all atoms in group atoms123 45: [ OK ] MindistTest.matrixWorks (0 ms) 45: [----------] 10 tests from MindistTest (23 ms total) 45: 45: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: trr version: GMX_trn_file (single precision) 45: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (5 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (2 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (1 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 45: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (1 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 45: Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (1 ms) 45: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 45: Group 0 ( System) has 6 elements 45: Group 1 ( Water) has 6 elements 45: Group 2 ( SOL) has 6 elements 45: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 45: Selected 0: 'System' 45: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) 45: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (13 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 22 tests from 4 test suites ran. (1161 ms total) 45: [ PASSED ] 22 tests. 45/81 Test #45: GmxAnaTest ..................................... Passed 1.64 sec test 46 Start 46: GmxPreprocessTests 46: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/GmxPreprocessTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests 46: Test timeout computed to be: 1920 46: [==========] Running 90 tests from 11 test suites. 46: [----------] Global test environment set-up. 46: [----------] 4 tests from GenconfTest 46: [ RUN ] GenconfTest.nbox_Works 46: [ OK ] GenconfTest.nbox_Works (0 ms) 46: [ RUN ] GenconfTest.nbox_norenumber_Works 46: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 46: [ RUN ] GenconfTest.nbox_dist_Works 46: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 46: [ RUN ] GenconfTest.nbox_rot_Works 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: center of geometry: 1.733667, 1.477000, 0.905167 46: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 46: [----------] 4 tests from GenconfTest (3 ms total) 46: 46: [----------] 2 tests from GenionTest 46: [ RUN ] GenionTest.HighConcentrationIonPlacement 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 46: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 46: buffer. The cluster pair list does have a buffering effect, but choosing 46: a larger rlist might be necessary for good energy conservation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: Generating 1-4 interactions: fudge = 0.5 46: Number of degrees of freedom in T-Coupling group rest is 1308.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 46: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 46: Group 0 ( System) has 653 elements 46: Group 1 ( Water) has 648 elements 46: Group 2 ( SOL) has 648 elements 46: Group 3 ( non-Water) has 5 elements 46: Group 4 ( Other) has 5 elements 46: Group 5 ( METH) has 5 elements 46: Select a group: Number of (3-atomic) solvent molecules: 216 46: Using random seed 1997. 46: Replacing solvent molecule 56 (atom 168) with NA 46: Replacing solvent molecule 120 (atom 360) with NA 46: Replacing solvent molecule 182 (atom 546) with NA 46: Replacing solvent molecule 71 (atom 213) with NA 46: Replacing solvent molecule 189 (atom 567) with CL 46: Replacing solvent molecule 54 (atom 162) with CL 46: Replacing solvent molecule 155 (atom 465) with CL 46: Replacing solvent molecule 99 (atom 297) with CL 46: 46: Setting the LD random seed to -268471312 46: 46: Generated 331705 of the 331705 non-bonded parameter combinations 46: 46: Generated 331705 of the 331705 1-4 parameter combinations 46: 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: 46: Excluding 3 bonded neighbours molecule type 'methane' 46: Analysing residue names: 46: There are: 216 Water residues 46: There are: 1 Other residues 46: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 46: 46: This run will generate roughly 0 Mb of data 46: Will try to add 4 NA ions and 4 CL ions. 46: Select a continuous group of solvent molecules 46: Selected 1: 'Water' 46: [ OK ] GenionTest.HighConcentrationIonPlacement (438 ms) 46: [ RUN ] GenionTest.NoIonPlacement 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 46: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 46: buffer. The cluster pair list does have a buffering effect, but choosing 46: a larger rlist might be necessary for good energy conservation. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: Generating 1-4 interactions: fudge = 0.5 46: Number of degrees of freedom in T-Coupling group rest is 1308.00 46: 46: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 46: You are using a plain Coulomb cut-off, which might produce artifacts. 46: You might want to consider using PME electrostatics. 46: 46: 46: 46: There were 3 notes 46: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 46: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 46: No ions to add, will just copy input configuration. 46: Setting the LD random seed to -1445906 46: 46: Generated 331705 of the 331705 non-bonded parameter combinations 46: 46: Generated 331705 of the 331705 1-4 parameter combinations 46: 46: Excluding 2 bonded neighbours molecule type 'SOL' 46: 46: Excluding 3 bonded neighbours molecule type 'methane' 46: Analysing residue names: 46: There are: 216 Water residues 46: There are: 1 Other residues 46: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 46: 46: This run will generate roughly 0 Mb of data 46: [ OK ] GenionTest.NoIonPlacement (422 ms) 46: [----------] 2 tests from GenionTest (860 ms total) 46: 46: [----------] 1 test from GenRestrTest 46: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 46: 46: Reading structure file 46: Group 0 ( System) has 156 elements 46: Group 1 ( Protein) has 156 elements 46: Group 2 ( Protein-H) has 75 elements 46: Group 3 ( C-alpha) has 10 elements 46: Group 4 ( Backbone) has 30 elements 46: Group 5 ( MainChain) has 40 elements 46: Group 6 ( MainChain+Cb) has 49 elements 46: Group 7 ( MainChain+H) has 52 elements 46: Group 8 ( SideChain) has 104 elements 46: Group 9 ( SideChain-H) has 35 elements 46: Select a group: Select group to position restrain 46: Selected 3: 'C-alpha' 46: [ OK ] GenRestrTest.SimpleRestraintsGenerated (2 ms) 46: [----------] 1 test from GenRestrTest (2 ms total) 46: 46: [----------] 9 tests from PreprocessingAtomTypesTest 46: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 46: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 46: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 46: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 46: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 46: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 46: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 46: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 46: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 46: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 46: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 46: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 46: 46: [----------] 10 tests from PreprocessingBondAtomTypeTest 46: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 46: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 46: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 46: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 46: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 46: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 46: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 46: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 46: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 46: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 46: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 46: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 46: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 46: 46: [----------] 1 test from GromppDirectiveTest 46: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 46: Ignoring obsolete mdp entry 'title' 46: Generating 1-4 interactions: fudge = 0.5 46: 46: NOTE 1 [file directives.top, line 44]: 46: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 46: any other atom in the same moleculetype. Although technically this might 46: not cause issues in a simulation, this often means that the user forgot 46: to add a bond/potential/constraint or put multiple molecules in the same 46: moleculetype definition by mistake. Run with -v to get information for 46: each atom. 46: 46: Number of degrees of freedom in T-Coupling group rest is 9.00 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 46: NVE simulation: will use the initial temperature of 300.000 K for 46: determining the Verlet buffer size 46: 46: 46: There were 2 notes 46: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 46: Setting the LD random seed to -1090520195 46: 46: Generated 10 of the 10 non-bonded parameter combinations 46: 46: Generated 10 of the 10 1-4 parameter combinations 46: 46: Excluding 0 bonded neighbours molecule type 'A' 46: 46: Setting gen_seed to -20189697 46: 46: Velocities were taken from a Maxwell distribution at 300 K 46: Analysing residue names: 46: There are: 1 Other residues 46: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 46: 46: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 46: 46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 46: 46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 46: 46: Note that mdrun will redetermine rlist based on the actual pair-list setup 46: 46: This run will generate roughly 0 Mb of data 46: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (5 ms) 46: [----------] 1 test from GromppDirectiveTest (5 ms total) 46: 46: [----------] 5 tests from InsertMoleculesTest 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 46: Reading solute configuration 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 8 atoms)! 46: 46: Added 1 molecules (out of 1 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 46: 46: Output configuration contains 8 atoms in 4 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (2 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 2 atoms)! 46: Try 2 success (now 4 atoms)! 46: Try 3 success (now 6 atoms)! 46: Try 4 success (now 8 atoms)! 46: Try 5 success (now 10 atoms)! 46: 46: Added 5 molecules (out of 5 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 46: 46: Output configuration contains 10 atoms in 10 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (1 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 46: Reading solute configuration 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 8 atoms)! 46: Try 2 success (now 10 atoms)! 46: 46: Added 2 molecules (out of 2 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 46: 46: Output configuration contains 10 atoms in 4 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (1 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 46: Reading solute configuration 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Try 1 success (now 650 atoms)! 46: Try 2 success (now 652 atoms)! 46: Try 3 success (now 654 atoms)! 46: Try 4 success (now 656 atoms)! 46: 46: Added 4 molecules (out of 4 requested) 46: Replaced 8 residues (24 atoms) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 46: 46: Output configuration contains 632 atoms in 212 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (10 ms) 46: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Using random seed 1997 46: Read 4 positions from file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 46: 46: Try 1 success (now 2 atoms)! 46: Try 2 success (now 4 atoms)! 46: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 46: Try 13 success (now 6 atoms)! 46: 46: Added 3 molecules (out of 4 requested) 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 46: 46: Output configuration contains 6 atoms in 3 residues 46: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (2 ms) 46: [----------] 5 tests from InsertMoleculesTest (18 ms total) 46: 46: [----------] 34 tests from GetIrTest 46: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 46: Ignoring obsolete mdp entry 'title' 46: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (3 ms) 46: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 46: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (0 ms) 46: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsKeyWithoutValue (3 ms) 46: [ RUN ] GetIrTest.RejectsValueWithoutKey 46: [ OK ] GetIrTest.RejectsValueWithoutKey (0 ms) 46: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 46: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (0 ms) 46: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (2 ms) 46: [ RUN ] GetIrTest.AcceptsEmptyLines 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsEmptyLines (2 ms) 46: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 46: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 46: [ RUN ] GetIrTest.MtsCheckNstenergy 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 46: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstenergy (5) 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.MtsCheckNstenergy (2 ms) 46: [ RUN ] GetIrTest.MtsCheckNstpcouple 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 46: Pressure coupling incorrect number of values (I need exactly 1) 46: 46: 46: ERROR 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 46: Pressure coupling incorrect number of values (I need exactly 1) 46: 46: 46: ERROR 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: With multiple time stepping, nstpcouple should be a mutiple of mts-factor 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: 46: ERROR 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: The Berendsen barostat does not generate any strictly correct ensemble, 46: and should not be used for new production simulations (in our opinion). 46: For isotropic scaling we would recommend the C-rescale barostat that also 46: ensures fast relaxation without oscillations, and for anisotropic scaling 46: you likely want to use the Parrinello-Rahman barostat. 46: 46: 46: ERROR 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 46: compressibility must be > 0 when using pressure coupling Berendsen 46: 46: 46: [ OK ] GetIrTest.MtsCheckNstpcouple (2 ms) 46: [ RUN ] GetIrTest.MtsCheckNstdhdl 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: Setting nstcalcenergy (100) equal to nstdhdl (5) 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: 46: ERROR 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 46: Lambda state must be set, either with init-lambda-state or with 46: init-lambda 46: 46: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 46: [ RUN ] GetIrTest.AcceptsElectricField 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsElectricField (2 ms) 46: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (2 ms) 46: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (2 ms) 46: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 46: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (0 ms) 46: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsImplicitSolventNo (2 ms) 46: [ RUN ] GetIrTest.RejectsImplicitSolventYes 46: [ OK ] GetIrTest.RejectsImplicitSolventYes (0 ms) 46: [ RUN ] GetIrTest.AcceptsMimic 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsMimic (2 ms) 46: [ RUN ] GetIrTest.AcceptsTransformationCoord 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 46: pull-coord2 has a non-zero force constant and is also referenced in 46: pull-coord1-expression. Make sure that this is intended. In most use 46: cases, the pull coordinates referenced by a transformation coordinate 46: should have their force constant set to zero. 46: 46: 46: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.AcceptsTransformationCoord (2 ms) 46: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 46: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (2 ms) 46: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 46: pull-coord2 can not use pull-coord1 in the transformation since this is a 46: constraint 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (2 ms) 46: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 46: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 46: 'transformation' 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (2 ms) 46: [ RUN ] GetIrTest.MissingTransformationCoordExpression 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 46: pull-coord1-expression not set for pull coordinate of geometry 46: 'transformation' 46: 46: 46: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 46: For a correct single-point energy evaluation with nsteps = 0, use 46: continuation = yes to avoid constraining the input coordinates. 46: 46: [ OK ] GetIrTest.MissingTransformationCoordExpression (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 46: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 46: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 46: in total 100001 steps. This is not compatible with using soft-core 46: potentials. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 46: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 46: won't change anymore after step 100000 until the end of the simulation 46: after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 46: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 46: won't change anymore after step 100000 until the end of the simulation 46: after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 46: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 46: components won't change anymore after step 100000 until the end of the 46: simulation after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 46: 46: ERROR 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 46: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 46: components won't change anymore after step 100000 until the end of the 46: simulation after 100001 steps. 46: 46: 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (2 ms) 46: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 46: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (2 ms) 46: [----------] 34 tests from GetIrTest (70 ms total) 46: 46: [----------] 5 tests from SolvateTest 46: [ RUN ] SolvateTest.cs_box_Works 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 1x1x1 boxes 46: Solvent box contains 270 atoms in 90 residues 46: Removed 129 solvent atoms due to solvent-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 47 residues 46: Generated solvent containing 141 atoms in 47 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 46: 46: Output configuration contains 141 atoms in 47 residues 46: Volume : 1.331 (nm^3) 46: Density : 1056.36 (g/l) 46: Number of solvent molecules: 47 46: 46: [ OK ] SolvateTest.cs_box_Works (8 ms) 46: [ RUN ] SolvateTest.cs_cp_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 2x2x2 boxes 46: Solvent box contains 3660 atoms in 1220 residues 46: Removed 987 solvent atoms due to solvent-solvent overlap 46: Removed 15 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 886 residues 46: Generated solvent containing 2658 atoms in 886 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 46: 46: Output configuration contains 2664 atoms in 888 residues 46: Volume : 27.2709 (nm^3) 46: Density : 974.777 (g/l) 46: Number of solvent molecules: 886 46: 46: [ OK ] SolvateTest.cs_cp_Works (42 ms) 46: [ RUN ] SolvateTest.cs_cp_p_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 2x2x2 boxes 46: Solvent box contains 3660 atoms in 1220 residues 46: Removed 987 solvent atoms due to solvent-solvent overlap 46: Removed 15 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 886 residues 46: Generated solvent containing 2658 atoms in 886 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 46: 46: Output configuration contains 2664 atoms in 888 residues 46: Volume : 27.2709 (nm^3) 46: Density : 974.777 (g/l) 46: Number of solvent molecules: 886 46: 46: Processing topology 46: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 46: [ OK ] SolvateTest.cs_cp_p_Works (53 ms) 46: [ RUN ] SolvateTest.shell_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 2x2x2 boxes 46: Solvent box contains 3660 atoms in 1220 residues 46: Removed 987 solvent atoms due to solvent-solvent overlap 46: Removed 1902 solvent atoms more than 1.000000 nm from solute. 46: Removed 15 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 1 molecule type: 46: SOL ( 3 atoms): 252 residues 46: Generated solvent containing 756 atoms in 252 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 46: 46: Output configuration contains 762 atoms in 254 residues 46: Volume : 27.2709 (nm^3) 46: Density : 279.3 (g/l) 46: Number of solvent molecules: 252 46: 46: [ OK ] SolvateTest.shell_Works (25 ms) 46: [ RUN ] SolvateTest.update_Topology_Works 46: Reading solute configuration 46: Reading solvent configuration 46: 46: Initialising inter-atomic distances... 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 46: from the source below. This means the results may be different 46: compared to previous GROMACS versions. 46: 46: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 46: A. Bondi 46: van der Waals Volumes and Radii 46: J. Phys. Chem. 68 (1964) pp. 441-451 46: -------- -------- --- Thank You --- -------- -------- 46: 46: Generating solvent configuration 46: Will generate new solvent configuration of 3x3x3 boxes 46: Solvent box contains 14952 atoms in 4984 residues 46: Removed 2787 solvent atoms due to solvent-solvent overlap 46: Removed 30 solvent atoms due to solute-solvent overlap 46: Sorting configuration 46: Found 2 different molecule types: 46: HOH ( 3 atoms): 1876 residues 46: SOL ( 3 atoms): 2169 residues 46: Generated solvent containing 0 atoms in 0 residues 46: Writing generated configuration to /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 46: 46: Output configuration contains 12141 atoms in 4047 residues 46: Volume : 125 (nm^3) 46: Density : 968.963 (g/l) 46: Number of solvent molecules: 4045 46: 46: Processing topology 46: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 46: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 46: [ OK ] SolvateTest.update_Topology_Works (206 ms) 46: [----------] 5 tests from SolvateTest (336 ms total) 46: 46: [----------] 1 test from TopDirTests 46: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 46: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 46: [----------] 1 test from TopDirTests (0 ms total) 46: 46: [----------] 18 tests from SinglePeptideFragments/EditconfTest 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (25 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (4 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (5 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (3 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (2 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (2 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (11 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (3 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (3 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (4 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (4 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (4 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (2 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (2 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (2 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (2 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (2 ms) 46: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 46: 46: Select a group for output: 46: Group 0 ( two_residues) has 23 elements 46: There is one group in the index 46: Note that major changes are planned in future for editconf, to improve usability and utility. 46: Read 252 atoms 46: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 46: No velocities found 46: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (2 ms) 46: [----------] 18 tests from SinglePeptideFragments/EditconfTest (89 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 90 tests from 11 test suites ran. (1386 ms total) 46: [ PASSED ] 90 tests. 46/81 Test #46: GmxPreprocessTests ............................. Passed 1.92 sec test 47 Start 47: Pdb2gmx1Test 47: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/Pdb2gmx1Test.xml" 47: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests 47: Test timeout computed to be: 1920 47: [==========] Running 30 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 30 tests from Oplsaa/Pdb2gmxTest 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 0 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (59 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 0 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (66 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 0 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (61 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 0 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (56 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 0 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (242 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Marked 124 virtual sites 47: Added 16 dummy masses 47: Added 26 new constraints 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 130 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (60 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Marked 132 virtual sites 47: Added 10 dummy masses 47: Added 19 new constraints 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 133 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (66 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Marked 123 virtual sites 47: Added 22 dummy masses 47: Added 35 new constraints 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 132 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Marked 111 virtual sites 47: Added 18 dummy masses 47: Added 31 new constraints 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 116 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (56 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Marked 447 virtual sites 47: Added 58 dummy masses 47: Added 101 new constraints 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 462 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip3p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (259 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 0 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (58 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 0 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (63 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 0 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (51 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 0 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (47 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 0 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (263 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Marked 124 virtual sites 47: Added 16 dummy masses 47: Added 26 new constraints 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 130 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (55 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Marked 132 virtual sites 47: Added 10 dummy masses 47: Added 19 new constraints 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 133 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (62 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Marked 123 virtual sites 47: Added 22 dummy masses 47: Added 35 new constraints 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 132 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (57 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Marked 111 virtual sites 47: Added 18 dummy masses 47: Added 31 new constraints 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 116 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (52 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Marked 447 virtual sites 47: Added 58 dummy masses 47: Added 101 new constraints 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 462 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip4p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (267 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 0 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (50 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 0 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (56 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 0 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (52 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 0 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (49 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 0 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (236 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 25 donors and 23 acceptors were found. 47: There are 41 hydrogen bonds 47: Will use HISE for residue 8 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS3 HIS8 47: SG9 NE251 47: HIS8 NE251 1.055 47: MET12 SD83 0.763 0.990 47: Marked 124 virtual sites 47: Added 16 dummy masses 47: Added 26 new constraints 47: Before cleaning: 653 pairs 47: Before cleaning: 663 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 47: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 128 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (128 atoms, 16 residues) 47: 47: Identified residue ALA2 as a starting terminus. 47: 47: Identified residue SER17 as a ending terminus. 47: Start terminus ALA-2: NH3+ 47: End terminus SER-17: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 252 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 254, now 254 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 663 dihedrals, 51 impropers, 457 angles 47: 650 pairs, 254 bonds and 130 virtual sites 47: 47: Total mass 1846.112 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (59 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 30 donors and 22 acceptors were found. 47: There are 36 hydrogen bonds 47: Will use HISE for residue 29 47: Will use HISE for residue 32 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS27 HIS29 47: SG90 NE2111 47: HIS29 NE2111 0.987 47: HIS32 NE2135 1.590 1.155 47: Marked 132 virtual sites 47: Added 10 dummy masses 47: Added 19 new constraints 47: Before cleaning: 748 pairs 47: Before cleaning: 778 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 47: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 149 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (149 atoms, 16 residues) 47: 47: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue THR18 as a starting terminus. 47: 47: Identified residue PHE33 as a ending terminus. 47: Start terminus THR-18: NH3+ 47: End terminus PHE-33: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 281 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 290, now 290 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 778 dihedrals, 72 impropers, 516 angles 47: 736 pairs, 290 bonds and 133 virtual sites 47: 47: Total mass 2088.357 a.m.u. 47: 47: Total charge 1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (72 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 22 acceptors were found. 47: There are 26 hydrogen bonds 47: Will use HISE for residue 45 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS45 47: NE295 47: MET46 SD102 1.078 47: Marked 123 virtual sites 47: Added 22 dummy masses 47: Added 35 new constraints 47: Before cleaning: 676 pairs 47: Before cleaning: 696 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 47: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 132 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (132 atoms, 16 residues) 47: 47: Identified residue ALA34 as a starting terminus. 47: 47: Identified residue ALA49 as a ending terminus. 47: Start terminus ALA-34: NH3+ 47: End terminus ALA-49: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 255 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 261, now 261 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 696 dihedrals, 56 impropers, 472 angles 47: 667 pairs, 261 bonds and 132 virtual sites 47: 47: Total mass 1861.128 a.m.u. 47: 47: Total charge -1.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 22 donors and 21 acceptors were found. 47: There are 30 hydrogen bonds 47: Will use HISE for residue 60 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: HIS60 47: NE285 47: CYS62 SG98 0.803 47: Marked 111 virtual sites 47: Added 18 dummy masses 47: Added 31 new constraints 47: Before cleaning: 603 pairs 47: Before cleaning: 618 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 47: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 47: 47: chain #res #atoms 47: 47: 1 ' ' 16 117 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 (117 atoms, 16 residues) 47: 47: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 47: 47: Identified residue LYS50 as a starting terminus. 47: 47: Identified residue PRO65 as a ending terminus. 47: Start terminus LYS-50: NH3+ 47: End terminus PRO-65: PRO-COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 16 residues with 228 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 232, now 232 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 618 dihedrals, 48 impropers, 419 angles 47: 597 pairs, 232 bonds and 116 virtual sites 47: 47: Total mass 1662.883 a.m.u. 47: 47: Total charge -0.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (58 ms) 47: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.r2b 47: All occupancies are one 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/atomtypes.atp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.rtp 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.hdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.n.tdb 47: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/oplsaa.ff/aminoacids.c.tdb 47: Analysing hydrogen-bonding network for automated assignment of histidine 47: protonation. 89 donors and 98 acceptors were found. 47: There are 129 hydrogen bonds 47: Will use HISE for residue 31 47: Will use HISE for residue 51 47: 8 out of 8 lines of specbond.dat converted successfully 47: Special Atom Distance matrix: 47: CYS25 HIS31 HIS51 47: SG14 NE264 NE2226 47: HIS31 NE264 1.921 47: HIS51 NE2226 1.498 2.650 47: CYS80 SG477 0.207 1.984 1.570 47: Linking CYS-25 SG-14 and CYS-80 SG-477... 47: Marked 447 virtual sites 47: Added 58 dummy masses 47: Added 101 new constraints 47: Before cleaning: 2499 pairs 47: Before cleaning: 2524 dihedrals 47: Using the Oplsaa force field in directory oplsaa.ff 47: 47: going to rename oplsaa.ff/aminoacids.r2b 47: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 47: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 47: 47: Analyzing pdb file 47: Splitting chemical chains based on TER records or chain id changing. 47: 47: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 47: 47: chain #res #atoms 47: 47: 1 'A' 58 488 47: 47: All occupancies are one 47: 47: Reading residue database... (Oplsaa) 47: 47: Processing chain 1 'A' (488 atoms, 58 residues) 47: 47: Identified residue ASN24 as a starting terminus. 47: 47: Identified residue ARG81 as a ending terminus. 47: Start terminus ASN-24: NH3+ 47: End terminus ARG-81: COO- 47: 47: Checking for duplicate atoms.... 47: 47: Generating any missing hydrogen atoms and/or adding termini. 47: 47: Now there are 58 residues with 936 atoms 47: 47: Making bonds... 47: 47: Number of bonds was 951, now 951 47: 47: Generating angles, dihedrals and pairs... 47: 47: Making cmap torsions... 47: 47: There are 2524 dihedrals, 208 impropers, 1704 angles 47: 2469 pairs, 951 bonds and 462 virtual sites 47: 47: Total mass 6908.578 a.m.u. 47: 47: Total charge -6.000 e 47: 47: Writing topology 47: 47: Writing coordinate file... 47: 47: --------- PLEASE NOTE ------------ 47: 47: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 47: 47: The Oplsaa force field and the tip5p water model are used. 47: 47: --------- ETON ESAELP ------------ 47: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (278 ms) 47: [----------] 30 tests from Oplsaa/Pdb2gmxTest (2955 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 30 tests from 1 test suite ran. (2955 ms total) 47: [ PASSED ] 30 tests. 47/81 Test #47: Pdb2gmx1Test ................................... Passed 3.51 sec test 48 Start 48: Pdb2gmx2Test 48: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/Pdb2gmx2Test.xml" 48: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests 48: Test timeout computed to be: 1920 48: [==========] Running 40 tests from 2 test suites. 48: [----------] Global test environment set-up. 48: [----------] 20 tests from G43a1/Pdb2gmxTest 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (57 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (59 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (62 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (59 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (167 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 37 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 37 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (65 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 53 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 51 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (69 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 36 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 36 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (65 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 33 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 31 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (62 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 146 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 137 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (174 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (61 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (67 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (61 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (166 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 37 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 305 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 165 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 172, now 167 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 77 impropers, 241 angles 48: 267 pairs, 167 bonds and 37 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (62 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 53 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 429 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 202 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 216, now 211 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 134 impropers, 316 angles 48: 273 pairs, 211 bonds and 51 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (71 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 36 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 349 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 168 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 179, now 174 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 102 impropers, 260 angles 48: 242 pairs, 174 bonds and 36 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (65 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 33 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 299 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 150 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 159, now 154 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 80 impropers, 227 angles 48: 232 pairs, 154 bonds and 31 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge 0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (63 ms) 48: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.rtp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos43a1.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 146 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1256 dihedrals 48: Using the Gromos43a1 force field in directory gromos43a1.ff 48: 48: going to rename gromos43a1.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos43a1) 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 635 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 655, now 650 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 350 impropers, 955 angles 48: 972 pairs, 650 bonds and 137 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos43a1 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (169 ms) 48: [----------] 20 tests from G43a1/Pdb2gmxTest (1699 ms total) 48: 48: [----------] 20 tests from G53a6/Pdb2gmxTest 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (71 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (74 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (70 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (69 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (168 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 39 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 39 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (69 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 57 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 55 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (79 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 38 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 38 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (73 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 35 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 33 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (68 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 150 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 141 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spc water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (178 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 0 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (71 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 0 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (76 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 0 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (72 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 0 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (68 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 0 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (171 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 25 donors and 23 acceptors were found. 48: There are 41 hydrogen bonds 48: Will use HISE for residue 8 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS3 HIS8 48: SG9 NE251 48: HIS8 NE251 1.055 48: MET12 SD83 0.763 0.990 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 39 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 267 pairs 48: Before cleaning: 312 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 48: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 128 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (128 atoms, 16 residues) 48: 48: Identified residue ALA2 as a starting terminus. 48: 48: Identified residue SER17 as a ending terminus. 48: Start terminus ALA-2: NH3+ 48: End terminus SER-17: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 167 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 174, now 169 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 90 dihedrals, 79 impropers, 245 angles 48: 267 pairs, 169 bonds and 39 virtual sites 48: 48: Total mass 1846.116 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (70 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 30 donors and 22 acceptors were found. 48: There are 36 hydrogen bonds 48: Will use HISE for residue 29 48: Will use HISE for residue 32 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS27 HIS29 48: SG90 NE2111 48: HIS29 NE2111 0.987 48: HIS32 NE2135 1.590 1.155 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 57 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 273 pairs 48: Before cleaning: 443 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 48: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 149 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (149 atoms, 16 residues) 48: 48: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue THR18 as a starting terminus. 48: 48: Identified residue PHE33 as a ending terminus. 48: Start terminus THR-18: NH3+ 48: End terminus PHE-33: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 206 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 220, now 215 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 93 dihedrals, 138 impropers, 324 angles 48: 273 pairs, 215 bonds and 55 virtual sites 48: 48: Total mass 2088.361 a.m.u. 48: 48: Total charge 1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (79 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 22 acceptors were found. 48: There are 26 hydrogen bonds 48: Will use HISE for residue 45 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS45 48: NE295 48: MET46 SD102 1.078 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 38 virtual sites 48: Added 4 dummy masses 48: Added 8 new constraints 48: 48: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 242 pairs 48: Before cleaning: 356 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 48: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 132 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (132 atoms, 16 residues) 48: 48: Identified residue ALA34 as a starting terminus. 48: 48: Identified residue ALA49 as a ending terminus. 48: Start terminus ALA-34: NH3+ 48: End terminus ALA-49: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 170 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 181, now 176 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 81 dihedrals, 104 impropers, 264 angles 48: 242 pairs, 176 bonds and 38 virtual sites 48: 48: Total mass 1861.132 a.m.u. 48: 48: Total charge -1.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (73 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 22 donors and 21 acceptors were found. 48: There are 30 hydrogen bonds 48: Will use HISE for residue 60 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: HIS60 48: NE285 48: CYS62 SG98 0.803 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 35 virtual sites 48: Added 4 dummy masses 48: Added 10 new constraints 48: 48: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 232 pairs 48: Before cleaning: 306 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 48: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 48: 48: chain #res #atoms 48: 48: 1 ' ' 16 117 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 (117 atoms, 16 residues) 48: 48: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 48: 48: Identified residue LYS50 as a starting terminus. 48: 48: Identified residue PRO65 as a ending terminus. 48: Start terminus LYS-50: NH3+ 48: End terminus PRO-65: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 16 residues with 152 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 161, now 156 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 78 dihedrals, 82 impropers, 231 angles 48: 232 pairs, 156 bonds and 33 virtual sites 48: 48: Total mass 1662.887 a.m.u. 48: 48: Total charge -0.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (71 ms) 48: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.r2b 48: All occupancies are one 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/atomtypes.atp 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.rtp 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.hdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.n.tdb 48: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/gromos53a6.ff/aminoacids.c.tdb 48: Analysing hydrogen-bonding network for automated assignment of histidine 48: protonation. 89 donors and 98 acceptors were found. 48: There are 129 hydrogen bonds 48: Will use HISE for residue 31 48: Will use HISE for residue 51 48: 8 out of 8 lines of specbond.dat converted successfully 48: Special Atom Distance matrix: 48: CYS25 HIS31 HIS51 48: SG14 NE264 NE2226 48: HIS31 NE264 1.921 48: HIS51 NE2226 1.498 2.650 48: CYS80 SG477 0.207 1.984 1.570 48: Linking CYS-25 SG-14 and CYS-80 SG-477... 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: 48: WARNING: Duplicate line found in or between hackblock and rtp entries 48: 48: Marked 150 virtual sites 48: Added 10 dummy masses 48: Added 29 new constraints 48: 48: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom H used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: 48: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 48: to an entry in the topology database, but the atom O used in 48: an interaction of type angle in that entry is not found in the 48: input file. Perhaps your atom and/or residue naming needs to be 48: fixed. 48: 48: 48: Before cleaning: 972 pairs 48: Before cleaning: 1270 dihedrals 48: Using the Gromos53a6 force field in directory gromos53a6.ff 48: 48: going to rename gromos53a6.ff/aminoacids.r2b 48: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 48: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 48: 48: Analyzing pdb file 48: Splitting chemical chains based on TER records or chain id changing. 48: 48: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 48: 48: chain #res #atoms 48: 48: 1 'A' 58 488 48: 48: All occupancies are one 48: 48: Reading residue database... (Gromos53a6) 48: 48: Using default: not generating all possible dihedrals 48: 48: Using default: excluding 3 bonded neighbors 48: 48: Using default: generating 1,4 H--H interactions 48: 48: Using default: removing proper dihedrals found on the same bond as a proper dihedral 48: 48: Processing chain 1 'A' (488 atoms, 58 residues) 48: 48: Identified residue ASN24 as a starting terminus. 48: 48: Identified residue ARG81 as a ending terminus. 48: Start terminus ASN-24: NH3+ 48: End terminus ARG-81: COO- 48: 48: Checking for duplicate atoms.... 48: 48: Generating any missing hydrogen atoms and/or adding termini. 48: 48: Now there are 58 residues with 639 atoms 48: 48: Making bonds... 48: 48: Number of bonds was 659, now 654 48: 48: Generating angles, dihedrals and pairs... 48: 48: Making cmap torsions... 48: 48: There are 321 dihedrals, 354 impropers, 963 angles 48: 972 pairs, 654 bonds and 141 virtual sites 48: 48: Total mass 6908.582 a.m.u. 48: 48: Total charge -6.000 e 48: 48: Writing topology 48: 48: Writing coordinate file... 48: 48: --------- PLEASE NOTE ------------ 48: 48: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 48: 48: The Gromos53a6 force field and the spce water model are used. 48: 48: --------- ETON ESAELP ------------ 48: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (178 ms) 48: [----------] 20 tests from G53a6/Pdb2gmxTest (1861 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 40 tests from 2 test suites ran. (3560 ms total) 48: [ PASSED ] 40 tests. 48/81 Test #48: Pdb2gmx2Test ................................... Passed 4.17 sec test 49 Start 49: Pdb2gmx3Test 49: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/Pdb2gmx3Test.xml" 49: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/gmxpreprocess/tests 49: Test timeout computed to be: 1920 49: [==========] Running 39 tests from 6 test suites. 49: [----------] Global test environment set-up. 49: [----------] 10 tests from Amber/Pdb2gmxTest 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 653 pairs 49: Before cleaning: 691 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 255, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 691 dihedrals, 51 impropers, 457 angles 49: 650 pairs, 254 bonds and 0 virtual sites 49: 49: Total mass 1846.132 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (64 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 748 pairs 49: Before cleaning: 788 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 291, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 788 dihedrals, 72 impropers, 516 angles 49: 736 pairs, 290 bonds and 0 virtual sites 49: 49: Total mass 2088.366 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (70 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 676 pairs 49: Before cleaning: 727 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 262, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 727 dihedrals, 56 impropers, 472 angles 49: 667 pairs, 261 bonds and 0 virtual sites 49: 49: Total mass 1861.124 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (65 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 603 pairs 49: Before cleaning: 634 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 233, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 634 dihedrals, 48 impropers, 419 angles 49: 597 pairs, 232 bonds and 0 virtual sites 49: 49: Total mass 1662.888 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (63 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Before cleaning: 2499 pairs 49: Before cleaning: 2631 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 952, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2631 dihedrals, 208 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 0 virtual sites 49: 49: Total mass 6908.576 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (239 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 124 virtual sites 49: Added 16 dummy masses 49: Added 26 new constraints 49: Before cleaning: 653 pairs 49: Before cleaning: 691 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 255, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 691 dihedrals, 51 impropers, 457 angles 49: 650 pairs, 254 bonds and 130 virtual sites 49: 49: Total mass 1846.132 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (72 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 132 virtual sites 49: Added 10 dummy masses 49: Added 19 new constraints 49: Before cleaning: 748 pairs 49: Before cleaning: 788 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 291, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 788 dihedrals, 72 impropers, 516 angles 49: 736 pairs, 290 bonds and 133 virtual sites 49: 49: Total mass 2088.366 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (70 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 123 virtual sites 49: Added 22 dummy masses 49: Added 35 new constraints 49: Before cleaning: 676 pairs 49: Before cleaning: 727 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 262, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 727 dihedrals, 56 impropers, 472 angles 49: 667 pairs, 261 bonds and 132 virtual sites 49: 49: Total mass 1861.124 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (72 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 111 virtual sites 49: Added 18 dummy masses 49: Added 31 new constraints 49: Before cleaning: 603 pairs 49: Before cleaning: 634 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 233, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 634 dihedrals, 48 impropers, 419 angles 49: 597 pairs, 232 bonds and 116 virtual sites 49: 49: Total mass 1662.888 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (61 ms) 49: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Marked 447 virtual sites 49: Added 58 dummy masses 49: Added 101 new constraints 49: Before cleaning: 2499 pairs 49: Before cleaning: 2631 dihedrals 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 952, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2631 dihedrals, 208 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 462 virtual sites 49: 49: Total mass 6908.576 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Amber99sb-ildn force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (279 ms) 49: [----------] 10 tests from Amber/Pdb2gmxTest (1061 ms total) 49: 49: [----------] 1 test from AmberTip4p/Pdb2gmxTest 49: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/amber99sb-ildn.ff/rna.arn 49: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 49: 49: going to rename amber99sb-ildn.ff/aminoacids.r2b 49: 49: going to rename amber99sb-ildn.ff/dna.r2b 49: 49: going to rename amber99sb-ildn.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 49: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 2 4 (only water) 49: 49: All occupancies are one 49: 49: Reading residue database... (Amber99sb-ildn) 49: 49: Processing chain 1 (4 atoms, 2 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 2 residues with 8 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 4, now 4 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 2 angles 49: 0 pairs, 4 bonds and 0 virtual sites 49: 49: Total mass 36.032 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 49: 49: The Amber99sb-ildn force field and the tip4p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (25 ms) 49: [----------] 1 test from AmberTip4p/Pdb2gmxTest (25 ms total) 49: 49: [----------] 12 tests from Charmm/Pdb2gmxTest 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 653 pairs 49: Before cleaning: 663 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 254, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 663 dihedrals, 48 impropers, 457 angles 49: 650 pairs, 254 bonds and 0 virtual sites 49: 49: Total mass 1846.115 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (57 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 748 pairs 49: Before cleaning: 778 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus PHE-33: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 290, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 778 dihedrals, 49 impropers, 516 angles 49: 736 pairs, 290 bonds and 0 virtual sites 49: 49: Total mass 2088.361 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (73 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 676 pairs 49: Before cleaning: 696 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: Start terminus ALA-34: NH3+ 49: End terminus ALA-49: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 261, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 696 dihedrals, 39 impropers, 472 angles 49: 667 pairs, 261 bonds and 0 virtual sites 49: 49: Total mass 1861.130 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (65 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 603 pairs 49: Before cleaning: 618 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: Start terminus LYS-50: NH3+ 49: End terminus PRO-65: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 232, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 618 dihedrals, 38 impropers, 419 angles 49: 597 pairs, 232 bonds and 0 virtual sites 49: 49: Total mass 1662.885 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (57 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 2499 pairs 49: Before cleaning: 2524 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: Start terminus ASN-24: NH3+ 49: End terminus ARG-81: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 951, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 56 cmap torsion pairs 49: 49: There are 2524 dihedrals, 149 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 0 virtual sites 49: 49: Total mass 6908.566 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (212 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 39 pairs 49: Before cleaning: 39 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb... 49: Read 'GLU', 9 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 49: 49: chain #res #atoms 49: 49: 1 'X' 1 9 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'X' (9 atoms, 1 residues) 49: 49: Identified residue GLU1 as a starting terminus. 49: 49: Identified residue GLU1 as a ending terminus. 49: Start terminus GLU-1: NH3+ 49: End terminus GLU-1: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 1 residues with 18 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 17, now 17 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 39 dihedrals, 2 impropers, 30 angles 49: 39 pairs, 17 bonds and 0 virtual sites 49: 49: Total mass 146.123 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (26 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 124 virtual sites 49: Added 16 dummy masses 49: Added 26 new constraints 49: Before cleaning: 653 pairs 49: Before cleaning: 663 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 128 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (128 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 252 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 254, now 254 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 663 dihedrals, 48 impropers, 457 angles 49: 650 pairs, 254 bonds and 130 virtual sites 49: 49: Total mass 1846.115 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/A.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (60 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 30 donors and 22 acceptors were found. 49: There are 36 hydrogen bonds 49: Will use HISE for residue 29 49: Will use HISE for residue 32 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS27 HIS29 49: SG90 NE2111 49: HIS29 NE2111 0.987 49: HIS32 NE2135 1.590 1.155 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 132 virtual sites 49: Added 10 dummy masses 49: Added 19 new constraints 49: Before cleaning: 748 pairs 49: Before cleaning: 778 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb... 49: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 149 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (149 atoms, 16 residues) 49: 49: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue PHE33 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus PHE-33: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 281 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 290, now 290 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 778 dihedrals, 49 impropers, 516 angles 49: 736 pairs, 290 bonds and 133 virtual sites 49: 49: Total mass 2088.361 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/B.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (74 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 22 acceptors were found. 49: There are 26 hydrogen bonds 49: Will use HISE for residue 45 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS45 49: NE295 49: MET46 SD102 1.078 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 123 virtual sites 49: Added 22 dummy masses 49: Added 35 new constraints 49: Before cleaning: 676 pairs 49: Before cleaning: 696 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb... 49: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 132 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (132 atoms, 16 residues) 49: 49: Identified residue ALA34 as a starting terminus. 49: 49: Identified residue ALA49 as a ending terminus. 49: Start terminus ALA-34: NH3+ 49: End terminus ALA-49: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 261, now 261 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 696 dihedrals, 39 impropers, 472 angles 49: 667 pairs, 261 bonds and 132 virtual sites 49: 49: Total mass 1861.130 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/C.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (67 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 22 donors and 21 acceptors were found. 49: There are 30 hydrogen bonds 49: Will use HISE for residue 60 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS60 49: NE285 49: CYS62 SG98 0.803 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 111 virtual sites 49: Added 18 dummy masses 49: Added 31 new constraints 49: Before cleaning: 603 pairs 49: Before cleaning: 618 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb... 49: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 49: 49: chain #res #atoms 49: 49: 1 ' ' 16 117 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 (117 atoms, 16 residues) 49: 49: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 49: 49: Identified residue LYS50 as a starting terminus. 49: 49: Identified residue PRO65 as a ending terminus. 49: Start terminus LYS-50: NH3+ 49: End terminus PRO-65: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 228 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 232, now 232 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 14 cmap torsion pairs 49: 49: There are 618 dihedrals, 38 impropers, 419 angles 49: 597 pairs, 232 bonds and 116 virtual sites 49: 49: Total mass 1662.885 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/D.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (61 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 89 donors and 98 acceptors were found. 49: There are 129 hydrogen bonds 49: Will use HISE for residue 31 49: Will use HISE for residue 51 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS25 HIS31 HIS51 49: SG14 NE264 NE2226 49: HIS31 NE264 1.921 49: HIS51 NE2226 1.498 2.650 49: CYS80 SG477 0.207 1.984 1.570 49: Linking CYS-25 SG-14 and CYS-80 SG-477... 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 447 virtual sites 49: Added 58 dummy masses 49: Added 101 new constraints 49: Before cleaning: 2499 pairs 49: Before cleaning: 2524 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb... 49: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 58 488 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (488 atoms, 58 residues) 49: 49: Identified residue ASN24 as a starting terminus. 49: 49: Identified residue ARG81 as a ending terminus. 49: Start terminus ASN-24: NH3+ 49: End terminus ARG-81: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 58 residues with 936 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 951, now 951 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 56 cmap torsion pairs 49: 49: There are 2524 dihedrals, 149 impropers, 1704 angles 49: 2469 pairs, 951 bonds and 462 virtual sites 49: 49: Total mass 6908.566 a.m.u. 49: 49: Total charge -6.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/E.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (255 ms) 49: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Marked 8 virtual sites 49: Added 2 dummy masses 49: Added 3 new constraints 49: Before cleaning: 39 pairs 49: Before cleaning: 39 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb... 49: Read 'GLU', 9 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 49: 49: chain #res #atoms 49: 49: 1 'X' 1 9 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'X' (9 atoms, 1 residues) 49: 49: Identified residue GLU1 as a starting terminus. 49: 49: Identified residue GLU1 as a ending terminus. 49: Start terminus GLU-1: NH3+ 49: End terminus GLU-1: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 1 residues with 18 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 17, now 17 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 39 dihedrals, 2 impropers, 30 angles 49: 39 pairs, 17 bonds and 9 virtual sites 49: 49: Total mass 146.123 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/monomer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (31 ms) 49: [----------] 12 tests from Charmm/Pdb2gmxTest (1044 ms total) 49: 49: [----------] 8 tests from ChainSep/Pdb2gmxTest 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 651 pairs 49: Before cleaning: 661 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on changing chain id only (ignoring TER records). 49: 49: Merged chains into joint molecule definitions at 2 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: Start terminus PHE-6: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 258 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 258, now 258 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 10 cmap torsion pairs 49: 49: There are 661 dihedrals, 46 impropers, 463 angles 49: 648 pairs, 258 bonds and 0 virtual sites 49: 49: Total mass 1882.146 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (69 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 123 pairs 49: Before cleaning: 123 dihedrals 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 10 donors and 7 acceptors were found. 49: There are 7 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: HIS8 49: NE223 49: MET12 SD55 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 317 pairs 49: Before cleaning: 322 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on changing chain id only (ignoring TER records). 49: 49: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 4 28 49: 49: 2 'B' 7 58 49: 49: 3 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (28 atoms, 4 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 4 residues with 51 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 50, now 50 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2 cmap torsion pairs 49: 49: There are 123 dihedrals, 9 impropers, 88 angles 49: 123 pairs, 50 bonds and 0 virtual sites 49: 49: Total mass 434.421 a.m.u. 49: 49: Total charge -2.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (58 atoms, 7 residues) 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus PHE-6: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 7 residues with 124 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 125, now 125 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 5 cmap torsion pairs 49: 49: There are 322 dihedrals, 19 impropers, 227 angles 49: 314 pairs, 125 bonds and 0 virtual sites 49: 49: Total mass 846.083 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 51 atoms 4 residues 49: 49: Including chain 2 in system: 124 atoms 7 residues 49: 49: Including chain 3 in system: 83 atoms 5 residues 49: 49: Now there are 258 atoms and 16 residues 49: 49: Total mass in system 1882.146 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (53 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 651 pairs 49: Before cleaning: 661 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records only (ignoring chain id). 49: 49: Merged chains into joint molecule definitions at 2 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ILE-9: COO- 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 258 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 258, now 258 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 10 cmap torsion pairs 49: 49: There are 661 dihedrals, 46 impropers, 463 angles 49: 648 pairs, 258 bonds and 0 virtual sites 49: 49: Total mass 1882.146 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (65 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 10 donors and 12 acceptors were found. 49: There are 13 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 49: SG9 49: HIS8 NE251 1.055 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 288 pairs 49: Before cleaning: 293 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 152 pairs 49: Before cleaning: 152 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records only (ignoring chain id). 49: 49: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 8 61 49: 49: 2 'B' 3 25 49: 49: 3 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (61 atoms, 8 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ILE-9: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 8 residues with 114 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 115, now 115 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 6 cmap torsion pairs 49: 49: There are 293 dihedrals, 23 impropers, 203 angles 49: 285 pairs, 115 bonds and 0 virtual sites 49: 49: Total mass 888.952 a.m.u. 49: 49: Total charge -2.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (25 atoms, 3 residues) 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 61 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 60, now 60 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 152 dihedrals, 5 impropers, 112 angles 49: 152 pairs, 60 bonds and 0 virtual sites 49: 49: Total mass 391.552 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 114 atoms 8 residues 49: 49: Including chain 2 in system: 61 atoms 3 residues 49: 49: Including chain 3 in system: 83 atoms 5 residues 49: 49: Now there are 258 atoms and 16 residues 49: 49: Total mass in system 1882.146 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (58 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 650 pairs 49: Before cleaning: 660 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Merged chains into joint molecule definitions at 3 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: Start terminus PHE-6: NH3+ 49: End terminus ILE-9: COO- 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 261 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 260, now 260 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 8 cmap torsion pairs 49: 49: There are 660 dihedrals, 45 impropers, 466 angles 49: 647 pairs, 260 bonds and 0 virtual sites 49: 49: Total mass 1900.162 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (67 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 123 pairs 49: Before cleaning: 123 dihedrals 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 6 donors and 4 acceptors were found. 49: There are 3 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 164 pairs 49: Before cleaning: 169 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 152 pairs 49: Before cleaning: 152 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 4 28 49: 49: 2 'B' 4 33 49: 49: 3 'B' 3 25 49: 49: 4 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (28 atoms, 4 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue GLU5 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus GLU-5: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 4 residues with 51 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 50, now 50 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2 cmap torsion pairs 49: 49: There are 123 dihedrals, 9 impropers, 88 angles 49: 123 pairs, 50 bonds and 0 virtual sites 49: 49: Total mass 434.421 a.m.u. 49: 49: Total charge -2.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (33 atoms, 4 residues) 49: 49: Identified residue PHE6 as a starting terminus. 49: 49: Identified residue ILE9 as a ending terminus. 49: Start terminus PHE-6: NH3+ 49: End terminus ILE-9: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 4 residues with 66 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 67, now 67 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 2 cmap torsion pairs 49: 49: There are 169 dihedrals, 13 impropers, 118 angles 49: 161 pairs, 67 bonds and 0 virtual sites 49: 49: Total mass 472.547 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'B' (25 atoms, 3 residues) 49: 49: Identified residue LYS10 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus LYS-10: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 61 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 60, now 60 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 152 dihedrals, 5 impropers, 112 angles 49: 152 pairs, 60 bonds and 0 virtual sites 49: 49: Total mass 391.552 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Processing chain 4 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 51 atoms 4 residues 49: 49: Including chain 2 in system: 66 atoms 4 residues 49: 49: Including chain 3 in system: 61 atoms 3 residues 49: 49: Including chain 4 in system: 83 atoms 5 residues 49: 49: Now there are 261 atoms and 16 residues 49: 49: Total mass in system 1900.162 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (56 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 25 donors and 23 acceptors were found. 49: There are 41 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 652 pairs 49: Before cleaning: 662 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records and chain id changing. 49: 49: Merged chains into joint molecule definitions at 1 places. 49: 49: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 16 127 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (127 atoms, 16 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus MET-12: COO- 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 255 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 256, now 256 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 12 cmap torsion pairs 49: 49: There are 662 dihedrals, 47 impropers, 460 angles 49: 649 pairs, 256 bonds and 0 virtual sites 49: 49: Total mass 1864.131 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (67 ms) 49: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: Analysing hydrogen-bonding network for automated assignment of histidine 49: protonation. 14 donors and 15 acceptors were found. 49: There are 20 hydrogen bonds 49: Will use HISE for residue 8 49: 8 out of 8 lines of specbond.dat converted successfully 49: Special Atom Distance matrix: 49: CYS3 HIS8 49: SG9 NE251 49: HIS8 NE251 1.055 49: MET12 SD83 0.763 0.990 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 441 pairs 49: Before cleaning: 446 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 211 pairs 49: Before cleaning: 216 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 49: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records and chain id changing. 49: 49: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 11 86 49: 49: 2 'C' 5 41 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (86 atoms, 11 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue MET12 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus MET-12: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 11 residues with 172 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 173, now 173 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 9 cmap torsion pairs 49: 49: There are 446 dihedrals, 29 impropers, 312 angles 49: 438 pairs, 173 bonds and 0 virtual sites 49: 49: Total mass 1262.488 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'C' (41 atoms, 5 residues) 49: 49: Identified residue ASN13 as a starting terminus. 49: 49: Identified residue SER17 as a ending terminus. 49: Start terminus ASN-13: NH3+ 49: End terminus SER-17: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 5 residues with 83 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 83, now 83 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 3 cmap torsion pairs 49: 49: There are 216 dihedrals, 18 impropers, 148 angles 49: 211 pairs, 83 bonds and 0 virtual sites 49: 49: Total mass 601.643 a.m.u. 49: 49: Total charge 1.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 172 atoms 11 residues 49: 49: Including chain 2 in system: 83 atoms 5 residues 49: 49: Now there are 255 atoms and 16 residues 49: 49: Total mass in system 1864.131 a.m.u. 49: 49: Total charge in system 0.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (55 ms) 49: [----------] 8 tests from ChainSep/Pdb2gmxTest (494 ms total) 49: 49: [----------] 4 tests from ChainChanges/Pdb2gmxTest 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on changing chain id only (ignoring TER records). 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (36 ms) 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records only (ignoring chain id). 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (37 ms) 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (34 ms) 49: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 83 pairs 49: Before cleaning: 83 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 145 pairs 49: Before cleaning: 150 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb... 49: Read 'Fragments of peptides and ions', 47 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records and chain id changing. 49: 49: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 3 19 49: 49: 2 'B' 3 28 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (19 atoms, 3 residues) 49: 49: Identified residue ALA2 as a starting terminus. 49: 49: Identified residue ASP4 as a ending terminus. 49: Start terminus ALA-2: NH3+ 49: End terminus ASP-4: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 36 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 35, now 35 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 83 dihedrals, 6 impropers, 61 angles 49: 83 pairs, 35 bonds and 0 virtual sites 49: 49: Total mass 306.314 a.m.u. 49: 49: Total charge -1.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'B' (28 atoms, 3 residues) 49: 49: Identified residue THR18 as a starting terminus. 49: 49: Identified residue TRP20 as a ending terminus. 49: Start terminus THR-18: NH3+ 49: End terminus TRP-20: COO- 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 3 residues with 57 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 58, now 58 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 1 cmap torsion pairs 49: 49: There are 150 dihedrals, 5 impropers, 103 angles 49: 142 pairs, 58 bonds and 0 virtual sites 49: 49: Total mass 404.468 a.m.u. 49: 49: Total charge -0.000 e 49: 49: Writing topology 49: 49: Including chain 1 in system: 36 atoms 3 residues 49: 49: Including chain 2 in system: 57 atoms 3 residues 49: 49: Now there are 93 atoms and 6 residues 49: 49: Total mass in system 710.782 a.m.u. 49: 49: Total charge in system -1.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/fragments.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (33 ms) 49: [----------] 4 tests from ChainChanges/Pdb2gmxTest (142 ms total) 49: 49: [----------] 4 tests from Cyclic/Pdb2gmxTest 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: WARNING: all CONECT records are ignored 49: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 6040 pairs 49: Before cleaning: 6605 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 6040 pairs 49: Before cleaning: 6605 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 49: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 49: 49: Moved all the water blocks to the end 49: 49: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 49: 49: chain #res #atoms 49: 49: 1 'P' 71 1527 49: 49: 2 'Q' 71 1527 49: 49: 3 'Q' 7 7 49: 49: 4 ' ' 10 10 (only water) 49: 49: 5 ' ' 16 16 (only water) 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'P' (1527 atoms, 71 residues) 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 71 residues with 2297 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 2481, now 2481 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 6605 dihedrals, 183 impropers, 4434 angles 49: 5827 pairs, 2481 bonds and 0 virtual sites 49: 49: Total mass 22984.514 a.m.u. 49: 49: Total charge -71.000 e 49: 49: Writing topology 49: 49: Processing chain 2 'Q' (1527 atoms, 71 residues) 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 71 residues with 2297 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: Number of bonds was 2481, now 2481 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 6605 dihedrals, 183 impropers, 4434 angles 49: 5827 pairs, 2481 bonds and 0 virtual sites 49: 49: Total mass 22984.514 a.m.u. 49: 49: Total charge -71.000 e 49: 49: Writing topology 49: 49: Processing chain 3 'Q' (7 atoms, 7 residues) 49: 49: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 49: 49: Disabling further notes about ions. 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 7 residues with 7 atoms 49: Chain time... 49: 49: Making bonds... 49: 49: No bonds 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 0 angles 49: 0 pairs, 0 bonds and 0 virtual sites 49: 49: Total mass 170.135 a.m.u. 49: 49: Total charge 14.000 e 49: 49: Writing topology 49: 49: Processing chain 4 (10 atoms, 10 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 10 residues with 30 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 30, now 30 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 30 angles 49: 0 pairs, 30 bonds and 0 virtual sites 49: 49: Total mass 180.154 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Processing chain 5 (16 atoms, 16 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 48 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 48, now 48 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 48 angles 49: 0 pairs, 48 bonds and 0 virtual sites 49: 49: Total mass 288.246 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Including chain 1 in system: 2297 atoms 71 residues 49: 49: Including chain 2 in system: 2297 atoms 71 residues 49: 49: Including chain 3 in system: 7 atoms 7 residues 49: 49: Including chain 4 in system: 30 atoms 10 residues 49: 49: Including chain 5 in system: 48 atoms 16 residues 49: 49: Now there are 4679 atoms and 175 residues 49: 49: Total mass in system 46607.562 a.m.u. 49: 49: Total charge in system -128.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (1804 ms) 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 2325 pairs 49: Before cleaning: 2325 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 49: Read 'CARNOCYCLIN-A', 413 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 60 413 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (413 atoms, 60 residues) 49: 49: Identified residue LEU1 as a starting terminus. 49: 49: Identified residue LEU60 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 60 residues with 878 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 880, now 880 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 60 cmap torsion pairs 49: 49: There are 2325 dihedrals, 137 impropers, 1614 angles 49: 2319 pairs, 880 bonds and 0 virtual sites 49: 49: Total mass 5866.087 a.m.u. 49: 49: Total charge 4.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (229 ms) 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: WARNING: all CONECT records are ignored 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 12080 pairs 49: Before cleaning: 13210 dihedrals 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 49: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: Moved all the water blocks to the end 49: 49: Merged chains into joint molecule definitions at 2 places. 49: 49: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 49: 49: chain #res #atoms 49: 49: 1 'P' 149 3061 49: 49: 2 ' ' 10 10 (only water) 49: 49: 3 ' ' 16 16 (only water) 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'P' (3061 atoms, 149 residues) 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Identified residue G1 as a starting terminus. 49: 49: Identified residue U71 as a ending terminus. 49: 49: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 49: 49: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 49: 49: Disabling further notes about ions. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 149 residues with 4601 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 4962, now 4962 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 13210 dihedrals, 366 impropers, 8868 angles 49: 11654 pairs, 4962 bonds and 0 virtual sites 49: 49: Total mass 46139.162 a.m.u. 49: 49: Total charge -128.000 e 49: 49: Writing topology 49: 49: Processing chain 2 (10 atoms, 10 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 10 residues with 30 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 30, now 30 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 30 angles 49: 0 pairs, 30 bonds and 0 virtual sites 49: 49: Total mass 180.154 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Processing chain 3 (16 atoms, 16 residues) 49: 49: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 16 residues with 48 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 48, now 48 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 0 dihedrals, 0 impropers, 48 angles 49: 0 pairs, 48 bonds and 0 virtual sites 49: 49: Total mass 288.246 a.m.u. 49: 49: Total charge 0.000 e 49: 49: Including chain 1 in system: 4601 atoms 149 residues 49: 49: Including chain 2 in system: 30 atoms 10 residues 49: 49: Including chain 3 in system: 48 atoms 16 residues 49: 49: Now there are 4679 atoms and 175 residues 49: 49: Total mass in system 46607.562 a.m.u. 49: 49: Total charge in system -128.000 e 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (3599 ms) 49: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.r2b 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.r2b 49: All occupancies are one 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/atomtypes.atp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.rtp 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/lipids.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.hdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.n.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.c.tdb 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.c.tdb 49: 8 out of 8 lines of specbond.dat converted successfully 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/aminoacids.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/dna.arn 49: Opening force field file /build/reproducible-path/gromacs-2022.5/share/top/charmm27.ff/rna.arn 49: Before cleaning: 2325 pairs 49: Before cleaning: 2325 dihedrals 49: Using the Charmm27 force field in directory charmm27.ff 49: 49: going to rename charmm27.ff/aminoacids.r2b 49: 49: going to rename charmm27.ff/rna.r2b 49: Reading /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 49: Read 'CARNOCYCLIN-A', 413 atoms 49: 49: Analyzing pdb file 49: Splitting chemical chains based on TER records or chain id changing. 49: 49: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 49: 49: chain #res #atoms 49: 49: 1 'A' 60 413 49: 49: All occupancies are one 49: 49: Reading residue database... (Charmm27) 49: 49: Processing chain 1 'A' (413 atoms, 60 residues) 49: 49: Identified residue LEU1 as a starting terminus. 49: 49: Identified residue LEU60 as a ending terminus. 49: 49: Checking for duplicate atoms.... 49: 49: Generating any missing hydrogen atoms and/or adding termini. 49: 49: Now there are 60 residues with 878 atoms 49: 49: Making bonds... 49: 49: Number of bonds was 880, now 880 49: 49: Generating angles, dihedrals and pairs... 49: 49: Making cmap torsions... 49: 49: There are 60 cmap torsion pairs 49: 49: There are 2325 dihedrals, 137 impropers, 1614 angles 49: 2319 pairs, 880 bonds and 0 virtual sites 49: 49: Total mass 5866.087 a.m.u. 49: 49: Total charge 4.000 e 49: 49: Writing topology 49: 49: Writing coordinate file... 49: 49: --------- PLEASE NOTE ------------ 49: 49: You have successfully generated a topology from: /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 49: 49: The Charmm27 force field and the tip3p water model are used. 49: 49: --------- ETON ESAELP ------------ 49: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (308 ms) 49: [----------] 4 tests from Cyclic/Pdb2gmxTest (5943 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 39 tests from 6 test suites ran. (8711 ms total) 49: [ PASSED ] 39 tests. 49/81 Test #49: Pdb2gmx3Test ................................... Passed 9.36 sec test 50 Start 50: CorrelationsTest 50: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/CorrelationsTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/correlationfunctions/tests 50: Test timeout computed to be: 30 50: [==========] Running 21 tests from 3 test suites. 50: [----------] Global test environment set-up. 50: [----------] 10 tests from AutocorrTest 50: [ RUN ] AutocorrTest.EacNormal 50: [ OK ] AutocorrTest.EacNormal (133 ms) 50: [ RUN ] AutocorrTest.EacNoNormalize 50: [ OK ] AutocorrTest.EacNoNormalize (63 ms) 50: [ RUN ] AutocorrTest.EacCos 50: [ OK ] AutocorrTest.EacCos (129 ms) 50: [ RUN ] AutocorrTest.EacVector 50: [ OK ] AutocorrTest.EacVector (199 ms) 50: [ RUN ] AutocorrTest.EacRcross 50: [ OK ] AutocorrTest.EacRcross (6 ms) 50: [ RUN ] AutocorrTest.EacP0 50: [ OK ] AutocorrTest.EacP0 (189 ms) 50: [ RUN ] AutocorrTest.EacP1 50: [ OK ] AutocorrTest.EacP1 (218 ms) 50: [ RUN ] AutocorrTest.EacP2 50: [ OK ] AutocorrTest.EacP2 (373 ms) 50: [ RUN ] AutocorrTest.EacP3 50: [ OK ] AutocorrTest.EacP3 (4 ms) 50: [ RUN ] AutocorrTest.EacP4 50: [ OK ] AutocorrTest.EacP4 (207 ms) 50: [----------] 10 tests from AutocorrTest (1527 ms total) 50: 50: [----------] 10 tests from ExpfitTest 50: [ RUN ] ExpfitTest.EffnEXP1 50: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 50: [ RUN ] ExpfitTest.EffnEXP2 50: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 50: [ RUN ] ExpfitTest.EffnEXPEXP 50: [ OK ] ExpfitTest.EffnEXPEXP (2 ms) 50: [ RUN ] ExpfitTest.EffnEXP5 50: [ OK ] ExpfitTest.EffnEXP5 (13 ms) 50: [ RUN ] ExpfitTest.EffnEXP7 50: [ OK ] ExpfitTest.EffnEXP7 (12 ms) 50: [ RUN ] ExpfitTest.EffnEXP9 50: [ OK ] ExpfitTest.EffnEXP9 (78 ms) 50: [ RUN ] ExpfitTest.EffnERF 50: [ OK ] ExpfitTest.EffnERF (6 ms) 50: [ RUN ] ExpfitTest.EffnERREST 50: [ OK ] ExpfitTest.EffnERREST (3 ms) 50: [ RUN ] ExpfitTest.EffnVAC 50: [ OK ] ExpfitTest.EffnVAC (16 ms) 50: [ RUN ] ExpfitTest.EffnPRES 50: [ OK ] ExpfitTest.EffnPRES (50 ms) 50: [----------] 10 tests from ExpfitTest (193 ms total) 50: 50: [----------] 1 test from ManyAutocorrelationTest 50: [ RUN ] ManyAutocorrelationTest.Empty 50: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 50: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 21 tests from 3 test suites ran. (1738 ms total) 50: [ PASSED ] 21 tests. 50/81 Test #50: CorrelationsTest ............................... Passed 2.73 sec test 51 Start 51: AnalysisDataUnitTests 51: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/AnalysisDataUnitTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/analysisdata/tests 51: Test timeout computed to be: 30 51: [==========] Running 69 tests from 14 test suites. 51: [----------] Global test environment set-up. 51: [----------] 3 tests from AnalysisDataInitializationTest 51: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 51: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 51: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 51: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 51: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 51: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 51: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 51: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 51: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/0 (3 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 51: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (9 ms) 51: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 51: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/1 (12 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 51: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (6 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 51: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 51: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/2 (11 ms total) 51: 51: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 51: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 51: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 51: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (9 ms) 51: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 51: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 51: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 51: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 51: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 51: [----------] 8 tests from AnalysisDataCommonTest/3 (13 ms total) 51: 51: [----------] 4 tests from AnalysisArrayDataTest 51: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 51: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 51: [ RUN ] AnalysisArrayDataTest.StorageWorks 51: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 51: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 51: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 51: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 51: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 51: [----------] 4 tests from AnalysisArrayDataTest (1 ms total) 51: 51: [----------] 6 tests from AverageModuleTest 51: [ RUN ] AverageModuleTest.BasicTest 51: [ OK ] AverageModuleTest.BasicTest (7 ms) 51: [ RUN ] AverageModuleTest.HandlesMultipointData 51: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 51: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 51: [ OK ] AverageModuleTest.HandlesMultipleDataSets (1 ms) 51: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 51: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 51: [ RUN ] AverageModuleTest.CanCustomizeXAxis 51: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 51: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 51: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 51: [----------] 6 tests from AverageModuleTest (11 ms total) 51: 51: [----------] 2 tests from FrameAverageModuleTest 51: [ RUN ] FrameAverageModuleTest.BasicTest 51: [ OK ] FrameAverageModuleTest.BasicTest (8 ms) 51: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 51: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (1 ms) 51: [----------] 2 tests from FrameAverageModuleTest (10 ms total) 51: 51: [----------] 7 tests from AnalysisHistogramSettingsTest 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 51: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 51: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 51: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 51: 51: [----------] 2 tests from SimpleHistogramModuleTest 51: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 51: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (1 ms) 51: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 51: [----------] 2 tests from SimpleHistogramModuleTest (8 ms total) 51: 51: [----------] 3 tests from WeightedHistogramModuleTest 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (1 ms) 51: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 51: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (1 ms) 51: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 51: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (1 ms) 51: [----------] 3 tests from WeightedHistogramModuleTest (4 ms total) 51: 51: [----------] 3 tests from BinAverageModuleTest 51: [ RUN ] BinAverageModuleTest.ComputesCorrectly 51: [ OK ] BinAverageModuleTest.ComputesCorrectly (1 ms) 51: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 51: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (1 ms) 51: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 51: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 51: [----------] 3 tests from BinAverageModuleTest (11 ms total) 51: 51: [----------] 4 tests from AbstractAverageHistogramTest 51: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 51: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (7 ms) 51: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 51: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (1 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (1 ms) 51: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 51: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (1 ms) 51: [----------] 4 tests from AbstractAverageHistogramTest (11 ms total) 51: 51: [----------] 3 tests from LifetimeModuleTest 51: [ RUN ] LifetimeModuleTest.BasicTest 51: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 51: [ RUN ] LifetimeModuleTest.CumulativeTest 51: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 51: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 51: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (9 ms) 51: [----------] 3 tests from LifetimeModuleTest (10 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 69 tests from 14 test suites ran. (112 ms total) 51: [ PASSED ] 69 tests. 51/81 Test #51: AnalysisDataUnitTests .......................... Passed 1.37 sec test 52 Start 52: CoordinateIOTests 52: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/CoordinateIOTests.xml" 52: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/coordinateio/tests 52: Test timeout computed to be: 30 52: [==========] Running 64 tests from 19 test suites. 52: [----------] Global test environment set-up. 52: [----------] 1 test from OutputSelectorDeathTest 52: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (5 ms) 52: [----------] 1 test from OutputSelectorDeathTest (5 ms total) 52: 52: [----------] 5 tests from TrajectoryFrameWriterTest 52: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (12 ms) 52: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (6 ms) 52: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (4 ms) 52: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (16 ms) 52: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 52: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 52: [----------] 5 tests from TrajectoryFrameWriterTest (41 ms total) 52: 52: [----------] 5 tests from OutputAdapterContainer 52: [ RUN ] OutputAdapterContainer.MakeEmpty 52: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 52: [ RUN ] OutputAdapterContainer.AddAdapter 52: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 52: [ RUN ] OutputAdapterContainer.RejectBadAdapter 52: [ OK ] OutputAdapterContainer.RejectBadAdapter (4 ms) 52: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 52: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 52: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 52: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 52: [----------] 5 tests from OutputAdapterContainer (4 ms total) 52: 52: [----------] 5 tests from FlagTest 52: [ RUN ] FlagTest.CanSetSimpleFlag 52: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 52: [ RUN ] FlagTest.CanAddNewBox 52: [ OK ] FlagTest.CanAddNewBox (0 ms) 52: [ RUN ] FlagTest.SetsImplicitPrecisionChange 52: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 52: [ RUN ] FlagTest.SetsImplicitStartTimeChange 52: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 52: [ RUN ] FlagTest.SetsImplicitTimeStepChange 52: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 52: [----------] 5 tests from FlagTest (0 ms total) 52: 52: [----------] 5 tests from SetAtomsTest 52: [ RUN ] SetAtomsTest.RemovesExistingAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.RemovesExistingAtoms (4 ms) 52: [ RUN ] SetAtomsTest.AddsNewAtoms 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.AddsNewAtoms (17 ms) 52: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (4 ms) 52: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (6 ms) 52: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (12 ms) 52: [----------] 5 tests from SetAtomsTest (45 ms total) 52: 52: [----------] 2 tests from SetBothTimeTest 52: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 52: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 52: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 52: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 52: [----------] 2 tests from SetBothTimeTest (0 ms total) 52: 52: [----------] 2 tests from SetStartTimeTest 52: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 52: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 52: [ RUN ] SetStartTimeTest.WorksWithZeroStart 52: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 52: [----------] 2 tests from SetStartTimeTest (0 ms total) 52: 52: [----------] 1 test from SetTimeStepTest 52: [ RUN ] SetTimeStepTest.SetTimeStepWorks 52: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 52: [----------] 1 test from SetTimeStepTest (0 ms total) 52: 52: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (6 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (13 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (4 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (12 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (16 ms) 52: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (12 ms) 52: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (66 ms total) 52: 52: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 52: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (4 ms) 52: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (12 ms) 52: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (8 ms) 52: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (25 ms total) 52: 52: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 52: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 52: 52: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (25 ms) 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (17 ms) 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (21 ms) 52: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (22 ms) 52: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (87 ms total) 52: 52: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 52: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (5 ms) 52: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (5 ms) 52: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (5 ms) 52: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (15 ms total) 52: 52: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 52: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 52: 52: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 52: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (5 ms) 52: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (5 ms) 52: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (10 ms total) 52: 52: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 52: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 52: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 52: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 52: 52: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 52: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (5 ms) 52: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (4 ms) 52: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (10 ms total) 52: 52: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 52: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 52: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 52: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 52: 52: [----------] 4 tests from ModuleSupported/NoOptionalOutput 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (6 ms) 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (4 ms) 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (4 ms) 52: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 52: 52: WARNING: Masses and atomic (Van der Waals) radii will be guessed 52: based on residue and atom names, since they could not be 52: definitively assigned from the information in your input 52: files. These guessed numbers might deviate from the mass 52: and radius of the atom type. Please check the output 52: files if necessary. Note, that this functionality may 52: be removed in a future GROMACS version. Please, consider 52: using another file format for your input. 52: 52: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (4 ms) 52: [----------] 4 tests from ModuleSupported/NoOptionalOutput (21 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 64 tests from 19 test suites ran. (335 ms total) 52: [ PASSED ] 64 tests. 52/81 Test #52: CoordinateIOTests .............................. Passed 1.49 sec test 53 Start 53: TrajectoryAnalysisUnitTests 53: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 53: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests 53: Test timeout computed to be: 1920 53: [==========] Running 96 tests from 17 test suites. 53: [----------] Global test environment set-up. 53: [----------] 11 tests from AngleModuleTest 53: [ RUN ] AngleModuleTest.ComputesSimpleAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesSimpleAngles (4 ms) 53: [ RUN ] AngleModuleTest.ComputesDihedrals 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesDihedrals (11 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorPairAngles (11 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (13 ms) 53: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (3 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (19 ms) 53: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 53: Reading frames from gro file 'Test system for different angles', 33 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (12 ms) 53: [ RUN ] AngleModuleTest.ComputesMultipleAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.ComputesMultipleAngles (5 ms) 53: [ RUN ] AngleModuleTest.HandlesDynamicSelections 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.HandlesDynamicSelections (15 ms) 53: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (4 ms) 53: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (13 ms) 53: [----------] 11 tests from AngleModuleTest (116 ms total) 53: 53: [----------] 5 tests from ClustsizeTest 53: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 53: There is one group in the index 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 24 53: cmid: 2, cmax: 4, max_size: 6 53: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 53: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (1 ms) 53: [ RUN ] ClustsizeTest.NoMolShortCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 53: There is one group in the index 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 24 53: cmid: 1, cmax: 6, max_size: 6 53: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 53: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (9 ms) 53: [ RUN ] ClustsizeTest.MolDefaultCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 8 53: cmid: 2, cmax: 4, max_size: 2 53: 50%100%cmid: 2, cmax: 6, max_size: 2 53: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (2 ms) 53: [ RUN ] ClustsizeTest.MolShortCutoff 53: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 8 53: cmid: 1, cmax: 6, max_size: 2 53: 50%100%cmid: 2, cmax: 6, max_size: 2 53: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (12 ms) 53: [ RUN ] ClustsizeTest.MolCSize 53: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Total number of atoms in clusters = 8 53: cmid: 2, cmax: 4, max_size: 2 53: 50%100%cmid: 2, cmax: 6, max_size: 2 53: 50%100%[ OK ] ClustsizeTest.MolCSize (2 ms) 53: [----------] 5 tests from ClustsizeTest (28 ms total) 53: 53: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 53: Reading frames from gro file 'Test system', 8 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (11 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 53: Reading frames from gro file 'Test system', 8 atoms. 53: Reading frame 0 time 0.000 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (7 ms) 53: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 53: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 53: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (20 ms total) 53: 53: [----------] 4 tests from ConvertTrjModuleTest 53: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (38 ms) 53: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (24 ms) 53: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (1 ms) 53: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 53: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 53: Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (11 ms) 53: [----------] 4 tests from ConvertTrjModuleTest (76 ms total) 53: 53: [----------] 6 tests from DistanceModuleTest 53: [ RUN ] DistanceModuleTest.ComputesDistances 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: atomname S1 S2: 53: Number of samples: 5 53: Average distance: 1.43246 nm 53: Standard deviation: 0.96700 nm 53: [ OK ] DistanceModuleTest.ComputesDistances (12 ms) 53: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: atomname S1 S2: 53: Number of samples: 5 53: Average distance: 1.43246 nm 53: Standard deviation: 0.96700 nm 53: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 53: Number of samples: 4 53: Average distance: 1.81066 nm 53: Standard deviation: 0.79289 nm 53: [ OK ] DistanceModuleTest.ComputesMultipleDistances (16 ms) 53: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: atomname S1 S2 and res_cog x < 2.8: 53: Number of samples: 3 53: Average distance: 1.72076 nm 53: Standard deviation: 1.24839 nm 53: [ OK ] DistanceModuleTest.HandlesDynamicSelections (8 ms) 53: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: Contacts: 53: Number of samples: 2 53: Average distance: 1.00000 nm 53: Standard deviation: 0.00000 nm 53: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (33 ms) 53: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: SuccessiveContacts: 53: Number of samples: 2 53: Average distance: 1.00000 nm 53: Standard deviation: 0.00000 nm 53: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (27 ms) 53: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: ManyContacts: 53: Number of samples: 10 53: Average distance: 1.82913 nm 53: Standard deviation: 0.78478 nm 53: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (30 ms) 53: [----------] 6 tests from DistanceModuleTest (133 ms total) 53: 53: [----------] 2 tests from ExtractClusterModuleTest 53: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 53: trr version: GMX_trn_file (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 53: Analyzed 26 frames, last time 0.050 53: There are 8 clusters containing 26 structures, highest framenr is 25 53: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (21 ms) 53: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 53: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 53: Analyzed 26 frames, last time 0.050 53: There are 8 clusters containing 26 structures, highest framenr is 25 53: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (6 ms) 53: [----------] 2 tests from ExtractClusterModuleTest (27 ms total) 53: 53: [----------] 2 tests from FreeVolumeModuleTest 53: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for CO2-RM. Set to zero. 53: Could not determine VDW radius for 40 particles. These were set to zero. 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: cutoff = 0.18 nm 53: probe_radius = 0 nm 53: seed = 13 53: ninsert = 1000 probes per nm^3 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 53: van der Spoel and Luciano T. Costa 53: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 53: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 53: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Free volume 38.02 +/- 0.00 % 53: Total volume 68.92 +/- 0.00 nm^3 53: Number of molecules 340 total mass 63491.38 Dalton 53: Average molar mass: 186.74 Dalton 53: Density rho: 1529.71 +/- 0.00 nm^3 53: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 53: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 53: Fractional free volume 0.194 +/- 0.000 53: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (343 ms) 53: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: cutoff = 0.18 nm 53: probe_radius = 0 nm 53: seed = 17 53: ninsert = 1000 probes per nm^3 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 53: van der Spoel and Luciano T. Costa 53: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 53: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 53: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Free volume 38.48 +/- 0.00 % 53: Total volume 68.92 +/- 0.00 nm^3 53: Number of molecules 340 total mass 63491.38 Dalton 53: Average molar mass: 186.74 Dalton 53: Density rho: 1529.71 +/- 0.00 nm^3 53: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 53: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 53: Fractional free volume 0.200 +/- 0.000 53: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (287 ms) 53: [----------] 2 tests from FreeVolumeModuleTest (631 ms total) 53: 53: [----------] 11 tests from MsdModuleTest 53: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.threeDimensionalDiffusion (3 ms) 53: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.twoDimensionalDiffusion (11 ms) 53: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.oneDimensionalDiffusion (7 ms) 53: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 53: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 53: Analyzed 10 frames, last time 9.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (11 ms) 53: [ RUN ] MsdModuleTest.multipleGroupsWork 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -1413592118 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.multipleGroupsWork (79 ms) 53: [ RUN ] MsdModuleTest.trestartLessThanDt 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartLessThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -136347817 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.trestartLessThanDt (81 ms) 53: [ RUN ] MsdModuleTest.trestartGreaterThanDt 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -66081 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.trestartGreaterThanDt (256 ms) 53: [ RUN ] MsdModuleTest.molTest 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to 1995431878 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.molTest (108 ms) 53: [ RUN ] MsdModuleTest.beginFit 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -10883169 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.beginFit (112 ms) 53: [ RUN ] MsdModuleTest.endFit 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -671089745 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.endFit (110 ms) 53: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 53: For energy conservation with LINCS, lincs_iter should be 2 or larger. 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 1818.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: NVE simulation: will use the initial temperature of 288.764 K for 53: determining the Verlet buffer size 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: There are 9 non-linear virtual site constructions. Their contribution to 53: the energy error is approximated. In most cases this does not affect the 53: error significantly. 53: 53: 53: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 5 notes 53: NOTE: You provided an index file 53: /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 53: (with -n), but it was not used by any selection. 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 53: Analyzed 21 frames, last time 40.000 53: Setting the LD random seed to -34603713 53: 53: Generated 2145 of the 2145 non-bonded parameter combinations 53: 53: Generated 2145 of the 2145 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 53: 53: Excluding 2 bonded neighbours molecule type 'SOL' 53: 53: Cleaning up constraints and constant bonded interactions with virtual sites 53: 53: Converted 15 Bonds with virtual sites to connections, 7 left 53: 53: Removed 18 Angles with virtual sites, 21 left 53: 53: Removed 10 Proper Dih.s with virtual sites, 44 left 53: 53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 53: 53: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 53: 53: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 53: 53: Note that mdrun will redetermine rlist based on the actual pair-list setup 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (101 ms) 53: [----------] 11 tests from MsdModuleTest (886 ms total) 53: 53: [----------] 9 tests from PairDistanceModuleTest 53: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesAllDistances (15 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (15 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (7 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (2 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (7 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (15 ms) 53: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (15 ms) 53: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (2 ms) 53: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (11 ms) 53: [----------] 9 tests from PairDistanceModuleTest (92 ms total) 53: 53: [----------] 5 tests from RdfModuleTest 53: [ RUN ] RdfModuleTest.BasicTest 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.BasicTest (89 ms) 53: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 53: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 53: Reading frame 0 time 0.000 Last frame 0 time 0.000 53: Analyzed 1 frames, last time 0.000 53: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (42 ms) 53: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (80 ms) 53: [ RUN ] RdfModuleTest.CalculatesSurf 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.CalculatesSurf (38 ms) 53: [ RUN ] RdfModuleTest.CalculatesXY 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] RdfModuleTest.CalculatesXY (83 ms) 53: [----------] 5 tests from RdfModuleTest (335 ms total) 53: 53: [----------] 5 tests from SasaModuleTest 53: [ RUN ] SasaModuleTest.BasicTest 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.BasicTest (35 ms) 53: [ RUN ] SasaModuleTest.HandlesSelectedResidues 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.HandlesSelectedResidues (21 ms) 53: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (16 ms) 53: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (32 ms) 53: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 53: Michael Scharf 53: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 53: of Surface Area and Volume and to Dot Surface Contouring of Molecular 53: Assemblies 53: J. Comp. Chem. 16 (1995) pp. 273-284 53: -------- -------- --- Thank You --- -------- -------- 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 53: from the source below. This means the results may be different 53: compared to previous GROMACS versions. 53: 53: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 53: A. Bondi 53: van der Waals Volumes and Radii 53: J. Phys. Chem. 68 (1964) pp. 441-451 53: -------- -------- --- Thank You --- -------- -------- 53: 53: Analyzed topology coordinates 53: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (27 ms) 53: [----------] 5 tests from SasaModuleTest (136 ms total) 53: 53: [----------] 8 tests from SelectModuleTest 53: [ RUN ] SelectModuleTest.BasicTest 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.BasicTest (14 ms) 53: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (8 ms) 53: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (12 ms) 53: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (4 ms) 53: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (12 ms) 53: [ RUN ] SelectModuleTest.NormalizesSizes 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.NormalizesSizes (7 ms) 53: [ RUN ] SelectModuleTest.WritesResidueNumbers 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.WritesResidueNumbers (11 ms) 53: [ RUN ] SelectModuleTest.WritesResidueIndices 53: Analyzed topology coordinates 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] SelectModuleTest.WritesResidueIndices (3 ms) 53: [----------] 8 tests from SelectModuleTest (75 ms total) 53: 53: [----------] 10 tests from SurfaceAreaTest 53: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 53: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 53: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 53: [ OK ] SurfaceAreaTest.ComputesTwoPoints (1 ms) 53: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 53: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (9 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints12 53: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints32 53: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints42 53: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 53: [ RUN ] SurfaceAreaTest.SurfacePoints122 53: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms) 53: [ RUN ] SurfaceAreaTest.Computes100Points 53: [ OK ] SurfaceAreaTest.Computes100Points (4 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (11 ms) 53: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 53: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (3 ms) 53: [----------] 10 tests from SurfaceAreaTest (33 ms total) 53: 53: [----------] 4 tests from TopologyInformation 53: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 53: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 53: [ RUN ] TopologyInformation.WorksWithGroFile 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TopologyInformation.WorksWithGroFile (12 ms) 53: [ RUN ] TopologyInformation.WorksWithPdbFile 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TopologyInformation.WorksWithPdbFile (8 ms) 53: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 53: 53: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 53: For a correct single-point energy evaluation with nsteps = 0, use 53: continuation = yes to avoid constraining the input coordinates. 53: 53: Generating 1-4 interactions: fudge = 0.5 53: 53: NOTE 2 [file lysozyme.top, line 1465]: 53: System has non-zero total charge: 2.000000 53: Total charge should normally be an integer. See 53: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 53: for discussion on how close it should be to an integer. 53: 53: 53: 53: Number of degrees of freedom in T-Coupling group rest is 465.00 53: 53: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 53: NVE simulation with an initial temperature of zero: will use a Verlet 53: buffer of 10%. Check your energy drift! 53: 53: 53: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 53: You are using a plain Coulomb cut-off, which might produce artifacts. 53: You might want to consider using PME electrostatics. 53: 53: 53: 53: There were 4 notes 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 53: Setting the LD random seed to 1876949500 53: 53: Generated 330891 of the 330891 non-bonded parameter combinations 53: 53: Generated 330891 of the 330891 1-4 parameter combinations 53: 53: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 53: Analysing residue names: 53: There are: 10 Protein residues 53: Analysing Protein... 53: 53: This run will generate roughly 0 Mb of data 53: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (2911 ms) 53: [----------] 4 tests from TopologyInformation (2932 ms total) 53: 53: [----------] 4 tests from TrajectoryModuleTest 53: [ RUN ] TrajectoryModuleTest.BasicTest 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.BasicTest (12 ms) 53: [ RUN ] TrajectoryModuleTest.PlotsXOnly 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.PlotsXOnly (8 ms) 53: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (7 ms) 53: [ RUN ] TrajectoryModuleTest.HandlesNoForces 53: Reading frames from gro file 'Test system', 15 atoms. 53: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 53: Analyzed 2 frames, last time 0.000 53: 53: WARNING: Masses and atomic (Van der Waals) radii will be guessed 53: based on residue and atom names, since they could not be 53: definitively assigned from the information in your input 53: files. These guessed numbers might deviate from the mass 53: and radius of the atom type. Please check the output 53: files if necessary. Note, that this functionality may 53: be removed in a future GROMACS version. Please, consider 53: using another file format for your input. 53: 53: [ OK ] TrajectoryModuleTest.HandlesNoForces (11 ms) 53: [----------] 4 tests from TrajectoryModuleTest (40 ms total) 53: 53: [----------] 5 tests from UnionFinderTest 53: [ RUN ] UnionFinderTest.WorksEmpty 53: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 53: [ RUN ] UnionFinderTest.BasicMerges 53: [ OK ] UnionFinderTest.BasicMerges (0 ms) 53: [ RUN ] UnionFinderTest.LargerMerges 53: [ OK ] UnionFinderTest.LargerMerges (0 ms) 53: [ RUN ] UnionFinderTest.LongRightMerge 53: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 53: [ RUN ] UnionFinderTest.LongLeftMerge 53: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 53: [----------] 5 tests from UnionFinderTest (0 ms total) 53: 53: [----------] 1 test from MappedUnionFinderTest 53: [ RUN ] MappedUnionFinderTest.BasicMerges 53: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 53: [----------] 1 test from MappedUnionFinderTest (0 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 96 tests from 17 test suites ran. (5568 ms total) 53: [ PASSED ] 96 tests. 53/81 Test #53: TrajectoryAnalysisUnitTests .................... Passed 6.94 sec test 54 Start 54: EnergyAnalysisUnitTests 54: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/EnergyAnalysisUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/energyanalysis/tests 54: Test timeout computed to be: 30 54: [==========] Running 7 tests from 4 test suites. 54: [----------] Global test environment set-up. 54: [----------] 1 test from DhdlTest 54: [ RUN ] DhdlTest.ExtractDhdl 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 54: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 54: Note: file tpx version 110, software tpx version 127 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 54: 54: 54: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 54: [ OK ] DhdlTest.ExtractDhdl (23 ms) 54: [----------] 1 test from DhdlTest (23 ms total) 54: 54: [----------] 1 test from OriresTest 54: [ RUN ] OriresTest.ExtractOrires 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 54: Reading file /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 54: Note: file tpx version 111, software tpx version 127 54: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 54: End your selection with 0 54: Selecting all 7 orientation restraints 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 54: [ OK ] OriresTest.ExtractOrires (30 ms) 54: [----------] 1 test from OriresTest (30 ms total) 54: 54: [----------] 3 tests from EnergyTest 54: [ RUN ] EnergyTest.ExtractEnergy 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: 54: Select the terms you want from the following list by 54: selecting either (part of) the name or the number or a combination. 54: End your selection with an empty line or a zero. 54: ------------------------------------------------------------------- 54: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 54: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 54: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 54: 13 Box-Z 14 Volume 15 Density 16 pV 54: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 54: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 54: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 54: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 54: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 54: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 54: 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 54: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 54: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 54: [ OK ] EnergyTest.ExtractEnergy (7 ms) 54: [ RUN ] EnergyTest.ExtractEnergyByNumber 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: 54: Select the terms you want from the following list by 54: selecting either (part of) the name or the number or a combination. 54: End your selection with an empty line or a zero. 54: ------------------------------------------------------------------- 54: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 54: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 54: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 54: 13 Box-Z 14 Volume 15 Density 16 pV 54: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 54: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 54: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 54: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 54: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 54: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 54: 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 54: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 54: Pres. DC -268.49 3 8.52175 13.2804 (bar) 54: [ OK ] EnergyTest.ExtractEnergyByNumber (7 ms) 54: [ RUN ] EnergyTest.ExtractEnergyMixed 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: 54: Select the terms you want from the following list by 54: selecting either (part of) the name or the number or a combination. 54: End your selection with an empty line or a zero. 54: ------------------------------------------------------------------- 54: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 54: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 54: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 54: 13 Box-Z 14 Volume 15 Density 16 pV 54: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 54: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 54: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 54: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 54: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 54: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 54: 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 54: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 54: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 54: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 54: [ OK ] EnergyTest.ExtractEnergyMixed (11 ms) 54: [----------] 3 tests from EnergyTest (26 ms total) 54: 54: [----------] 2 tests from ViscosityTest 54: [ RUN ] ViscosityTest.EinsteinViscosity 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Pres-XX 20.2092 65 717.193 185.978 (bar) 54: Pres-XY -47.7351 39 372.522 207.456 (bar) 54: Pres-XZ 11.477 31 379.79 6.80818 (bar) 54: Pres-YX -47.7106 39 372.525 207.5 (bar) 54: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 54: Pres-YZ -41.3534 45 401.216 114.663 (bar) 54: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 54: Pres-ZY -41.3119 45 401.196 114.743 (bar) 54: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 54: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 54: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 54: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 54: [ OK ] ViscosityTest.EinsteinViscosity (289 ms) 54: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 54: Opened /build/reproducible-path/gromacs-2022.5/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 54: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 54: 54: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 54: All statistics are over 5001 points 54: 54: Energy Average Err.Est. RMSD Tot-Drift 54: ------------------------------------------------------------------------------- 54: Pres-XX 20.2092 65 717.193 185.978 (bar) 54: Pres-XY -47.7351 39 372.522 207.456 (bar) 54: Pres-XZ 11.477 31 379.79 6.80818 (bar) 54: Pres-YX -47.7106 39 372.525 207.5 (bar) 54: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 54: Pres-YZ -41.3534 45 401.216 114.663 (bar) 54: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 54: Pres-ZY -41.3119 45 401.196 114.743 (bar) 54: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 54: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 54: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 54: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 54: [ OK ] ViscosityTest.EinsteinViscosityIntegral (257 ms) 54: [----------] 2 tests from ViscosityTest (546 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 7 tests from 4 test suites ran. (628 ms total) 54: [ PASSED ] 7 tests. 54/81 Test #54: EnergyAnalysisUnitTests ........................ Passed 1.91 sec test 55 Start 55: ToolUnitTests 55: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/ToolUnitTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests 55: Test timeout computed to be: 1920 55: [==========] Running 54 tests from 6 test suites. 55: [----------] Global test environment set-up. 55: [----------] 2 tests from DumpTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Setting the LD random seed to -214530 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: [ RUN ] DumpTest.WorksWithTpr 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 55: inputrec: 55: integrator = md 55: tinit = 0 55: dt = 0.001 55: nsteps = 0 55: init-step = 0 55: simulation-part = 1 55: mts = false 55: comm-mode = Linear 55: nstcomm = 100 55: bd-fric = 0 55: ld-seed = -214530 55: emtol = 10 55: emstep = 0.01 55: niter = 20 55: fcstep = 0 55: nstcgsteep = 1000 55: nbfgscorr = 10 55: rtpi = 0.05 55: nstxout = 0 55: nstvout = 0 55: nstfout = 0 55: nstlog = 1000 55: nstcalcenergy = 100 55: nstenergy = 1000 55: nstxout-compressed = 0 55: compressed-x-precision = 1000 55: cutoff-scheme = Verlet 55: nstlist = 10 55: pbc = xyz 55: periodic-molecules = false 55: verlet-buffer-tolerance = -1 55: rlist = 1.1 55: coulombtype = Cut-off 55: coulomb-modifier = Potential-shift 55: rcoulomb-switch = 0 55: rcoulomb = 1 55: epsilon-r = 1 55: epsilon-rf = inf 55: vdw-type = Cut-off 55: vdw-modifier = Potential-shift 55: rvdw-switch = 0 55: rvdw = 1 55: DispCorr = No 55: table-extension = 1 55: fourierspacing = 0.12 55: fourier-nx = 0 55: fourier-ny = 0 55: fourier-nz = 0 55: pme-order = 4 55: ewald-rtol = 1e-05 55: ewald-rtol-lj = 0.001 55: lj-pme-comb-rule = Geometric 55: ewald-geometry = 3d 55: epsilon-surface = 0 55: tcoupl = No 55: nsttcouple = -1 55: nh-chain-length = 0 55: print-nose-hoover-chain-variables = false 55: pcoupl = No 55: pcoupltype = Isotropic 55: nstpcouple = -1 55: tau-p = 1 55: compressibility (3x3): 55: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: ref-p (3x3): 55: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: refcoord-scaling = No 55: posres-com (3): 55: posres-com[0]= 0.00000e+00 55: posres-com[1]= 0.00000e+00 55: posres-com[2]= 0.00000e+00 55: posres-comB (3): 55: posres-comB[0]= 0.00000e+00 55: posres-comB[1]= 0.00000e+00 55: posres-comB[2]= 0.00000e+00 55: QMMM = false 55: qm-opts: 55: ngQM = 0 55: constraint-algorithm = Lincs 55: continuation = false 55: Shake-SOR = false 55: shake-tol = 0.0001 55: lincs-order = 4 55: lincs-iter = 1 55: lincs-warnangle = 30 55: nwall = 0 55: wall-type = 9-3 55: wall-r-linpot = -1 55: wall-atomtype[0] = -1 55: wall-atomtype[1] = -1 55: wall-density[0] = 0 55: wall-density[1] = 0 55: wall-ewald-zfac = 3 55: pull = false 55: awh = false 55: rotation = false 55: interactiveMD = false 55: disre = No 55: disre-weighting = Conservative 55: disre-mixed = false 55: dr-fc = 1000 55: dr-tau = 0 55: nstdisreout = 100 55: orire-fc = 0 55: orire-tau = 0 55: nstorireout = 100 55: free-energy = no 55: cos-acceleration = 0 55: deform (3x3): 55: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: simulated-tempering = false 55: swapcoords = no 55: userint1 = 0 55: userint2 = 0 55: userint3 = 0 55: userint4 = 0 55: userreal1 = 0 55: userreal2 = 0 55: userreal3 = 0 55: userreal4 = 0 55: applied-forces: 55: electric-field: 55: x: 55: E0 = 0 55: omega = 0 55: t0 = 0 55: sigma = 0 55: y: 55: E0 = 0 55: omega = 0 55: t0 = 0 55: sigma = 0 55: z: 55: E0 = 0 55: omega = 0 55: t0 = 0 55: sigma = 0 55: density-guided-simulation: 55: active = false 55: group = protein 55: similarity-measure = inner-product 55: atom-spreading-weight = unity 55: force-constant = 1e+09 55: gaussian-transform-spreading-width = 0.2 55: gaussian-transform-spreading-range-in-multiples-of-width = 4 55: reference-density-filename = reference.mrc 55: nst = 1 55: normalize-densities = true 55: adaptive-force-scaling = false 55: adaptive-force-scaling-time-constant = 4 55: shift-vector = 55: transformation-matrix = 55: qmmm-cp2k: 55: active = false 55: qmgroup = System 55: qmmethod = PBE 55: qmfilenames = 55: qmcharge = 0 55: qmmultiplicity = 1 55: grpopts: 55: nrdf: 465 55: ref-t: 0 55: tau-t: 0 55: annealing: No 55: annealing-npoints: 0 55: acc: 0 0 0 55: nfreeze: N N N 55: energygrp-flags[ 0]: 0 55: header: 55: bIr = present 55: bBox = present 55: bTop = present 55: bX = present 55: bV = present 55: bF = not present 55: natoms = 156 55: lambda = 0.000000e+00 55: buffer size = 59646 55: topology: 55: name="First 10 residues from 1AKI" 55: #atoms = 156 55: #molblock = 1 55: molblock (0): 55: moltype = 0 "Protein_chain_B" 55: #molecules = 1 55: #posres_xA = 0 55: #posres_xB = 0 55: bIntermolecularInteractions = false 55: ffparams: 55: atnr=10 55: ntypes=212 55: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 55: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 55: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 55: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 55: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 55: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 55: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 55: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 55: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 55: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 55: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 55: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 55: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 55: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 55: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 55: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 55: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 55: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 55: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 55: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 55: functype[33]=LJ_SR, c6= 1.22578131e-04, 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functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 55: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 55: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 55: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 55: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 55: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 55: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 55: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 55: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 55: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 55: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 55: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 55: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 55: functype[64]=LJ_SR, c6= 3.38512054e-03, 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functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 55: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 55: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 55: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 55: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 55: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 55: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 55: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 55: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 55: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 55: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 55: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 55: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 55: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 55: functype[95]=LJ_SR, c6= 6.04976481e-03, 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2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 55: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 55: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 55: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 55: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 55: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 55: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 55: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 55: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 55: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 55: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 55: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 55: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 55: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 55: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 55: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 55: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 55: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 55: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 55: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 55: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 55: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 55: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 55: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 55: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 55: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 55: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 55: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 55: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 55: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 55: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 55: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 55: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 55: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 55: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 55: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 55: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 55: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 55: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 55: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 55: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 55: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 55: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 55: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 55: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 55: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 55: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 55: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 55: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 55: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 55: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 55: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 55: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 55: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 55: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 55: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 55: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 55: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 55: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 55: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 55: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 55: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 55: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 55: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 55: reppow = 12 55: fudgeQQ = 0.5 55: cmap 55: atomtypes: 55: atomtype[ 0]={atomnumber= 7} 55: atomtype[ 1]={atomnumber= 1} 55: atomtype[ 2]={atomnumber= 6} 55: atomtype[ 3]={atomnumber= 1} 55: atomtype[ 4]={atomnumber= 6} 55: atomtype[ 5]={atomnumber= 8} 55: atomtype[ 6]={atomnumber= 6} 55: atomtype[ 7]={atomnumber= 1} 55: atomtype[ 8]={atomnumber= 6} 55: atomtype[ 9]={atomnumber= 16} 55: moltype (0): 55: name="Protein_chain_B" 55: atoms: 55: atom (156): 55: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 55: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 55: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 55: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 55: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 55: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 55: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 55: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 55: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 55: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 55: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 55: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 55: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 55: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 55: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 55: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 55: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 55: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 55: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 55: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 55: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 55: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 55: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 55: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 55: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 55: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 55: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 55: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 55: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 55: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 55: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 55: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 55: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 55: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 55: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 55: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 55: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 55: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 55: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 55: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 55: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 55: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 55: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 55: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 55: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 55: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 55: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 55: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 55: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 55: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 55: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 55: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 55: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 55: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 55: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 55: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 55: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 55: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 55: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 55: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 55: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 55: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 55: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 55: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 55: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 55: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 55: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 55: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 55: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 55: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 55: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 55: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 55: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 55: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 55: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 55: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 55: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 55: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 55: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 55: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 55: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 55: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 55: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 55: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 55: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 55: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 55: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 55: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 55: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 55: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 55: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 55: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 55: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 55: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 55: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 55: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 55: atom (156): 55: atom[0]={name="N"} 55: atom[1]={name="H1"} 55: atom[2]={name="H2"} 55: atom[3]={name="H3"} 55: atom[4]={name="CA"} 55: atom[5]={name="HA"} 55: atom[6]={name="CB"} 55: atom[7]={name="HB1"} 55: atom[8]={name="HB2"} 55: atom[9]={name="CG"} 55: atom[10]={name="HG1"} 55: atom[11]={name="HG2"} 55: atom[12]={name="CD"} 55: atom[13]={name="HD1"} 55: atom[14]={name="HD2"} 55: atom[15]={name="CE"} 55: atom[16]={name="HE1"} 55: atom[17]={name="HE2"} 55: atom[18]={name="NZ"} 55: atom[19]={name="HZ1"} 55: atom[20]={name="HZ2"} 55: atom[21]={name="HZ3"} 55: atom[22]={name="C"} 55: atom[23]={name="O"} 55: atom[24]={name="N"} 55: atom[25]={name="H"} 55: atom[26]={name="CA"} 55: atom[27]={name="HA"} 55: atom[28]={name="CB"} 55: atom[29]={name="HB"} 55: atom[30]={name="CG1"} 55: atom[31]={name="HG11"} 55: atom[32]={name="HG12"} 55: atom[33]={name="HG13"} 55: atom[34]={name="CG2"} 55: atom[35]={name="HG21"} 55: atom[36]={name="HG22"} 55: atom[37]={name="HG23"} 55: atom[38]={name="C"} 55: atom[39]={name="O"} 55: atom[40]={name="N"} 55: atom[41]={name="H"} 55: atom[42]={name="CA"} 55: atom[43]={name="HA"} 55: atom[44]={name="CB"} 55: atom[45]={name="HB1"} 55: atom[46]={name="HB2"} 55: atom[47]={name="CG"} 55: atom[48]={name="CD1"} 55: atom[49]={name="HD1"} 55: atom[50]={name="CD2"} 55: atom[51]={name="HD2"} 55: atom[52]={name="CE1"} 55: atom[53]={name="HE1"} 55: atom[54]={name="CE2"} 55: atom[55]={name="HE2"} 55: atom[56]={name="CZ"} 55: atom[57]={name="HZ"} 55: atom[58]={name="C"} 55: atom[59]={name="O"} 55: atom[60]={name="N"} 55: atom[61]={name="H"} 55: atom[62]={name="CA"} 55: atom[63]={name="HA1"} 55: atom[64]={name="HA2"} 55: atom[65]={name="C"} 55: atom[66]={name="O"} 55: atom[67]={name="N"} 55: atom[68]={name="H"} 55: atom[69]={name="CA"} 55: atom[70]={name="HA"} 55: atom[71]={name="CB"} 55: atom[72]={name="HB1"} 55: atom[73]={name="HB2"} 55: atom[74]={name="CG"} 55: atom[75]={name="HG1"} 55: atom[76]={name="HG2"} 55: atom[77]={name="CD"} 55: atom[78]={name="HD1"} 55: atom[79]={name="HD2"} 55: atom[80]={name="NE"} 55: atom[81]={name="HE"} 55: atom[82]={name="CZ"} 55: atom[83]={name="NH1"} 55: atom[84]={name="HH11"} 55: atom[85]={name="HH12"} 55: atom[86]={name="NH2"} 55: atom[87]={name="HH21"} 55: atom[88]={name="HH22"} 55: atom[89]={name="C"} 55: atom[90]={name="O"} 55: atom[91]={name="N"} 55: atom[92]={name="H"} 55: atom[93]={name="CA"} 55: atom[94]={name="HA"} 55: atom[95]={name="CB"} 55: atom[96]={name="HB1"} 55: atom[97]={name="HB2"} 55: atom[98]={name="SG"} 55: atom[99]={name="HG"} 55: atom[100]={name="C"} 55: atom[101]={name="O"} 55: atom[102]={name="N"} 55: atom[103]={name="H"} 55: atom[104]={name="CA"} 55: atom[105]={name="HA"} 55: atom[106]={name="CB"} 55: atom[107]={name="HB1"} 55: atom[108]={name="HB2"} 55: atom[109]={name="CG"} 55: atom[110]={name="HG1"} 55: atom[111]={name="HG2"} 55: atom[112]={name="CD"} 55: atom[113]={name="OE1"} 55: atom[114]={name="OE2"} 55: atom[115]={name="C"} 55: atom[116]={name="O"} 55: atom[117]={name="N"} 55: atom[118]={name="H"} 55: atom[119]={name="CA"} 55: atom[120]={name="HA"} 55: atom[121]={name="CB"} 55: atom[122]={name="HB1"} 55: atom[123]={name="HB2"} 55: atom[124]={name="CG"} 55: atom[125]={name="HG"} 55: atom[126]={name="CD1"} 55: atom[127]={name="HD11"} 55: atom[128]={name="HD12"} 55: atom[129]={name="HD13"} 55: atom[130]={name="CD2"} 55: atom[131]={name="HD21"} 55: atom[132]={name="HD22"} 55: atom[133]={name="HD23"} 55: atom[134]={name="C"} 55: atom[135]={name="O"} 55: atom[136]={name="N"} 55: atom[137]={name="H"} 55: atom[138]={name="CA"} 55: atom[139]={name="HA"} 55: atom[140]={name="CB"} 55: atom[141]={name="HB1"} 55: atom[142]={name="HB2"} 55: atom[143]={name="HB3"} 55: atom[144]={name="C"} 55: atom[145]={name="O"} 55: atom[146]={name="N"} 55: atom[147]={name="H"} 55: atom[148]={name="CA"} 55: atom[149]={name="HA"} 55: atom[150]={name="CB"} 55: atom[151]={name="HB1"} 55: atom[152]={name="HB2"} 55: atom[153]={name="HB3"} 55: atom[154]={name="C"} 55: atom[155]={name="O"} 55: type (156): 55: type[0]={name="opls_287",nameB="opls_287"} 55: type[1]={name="opls_290",nameB="opls_290"} 55: type[2]={name="opls_290",nameB="opls_290"} 55: type[3]={name="opls_290",nameB="opls_290"} 55: type[4]={name="opls_293B",nameB="opls_293B"} 55: type[5]={name="opls_140",nameB="opls_140"} 55: type[6]={name="opls_136",nameB="opls_136"} 55: type[7]={name="opls_140",nameB="opls_140"} 55: type[8]={name="opls_140",nameB="opls_140"} 55: type[9]={name="opls_136",nameB="opls_136"} 55: type[10]={name="opls_140",nameB="opls_140"} 55: type[11]={name="opls_140",nameB="opls_140"} 55: type[12]={name="opls_136",nameB="opls_136"} 55: type[13]={name="opls_140",nameB="opls_140"} 55: type[14]={name="opls_140",nameB="opls_140"} 55: type[15]={name="opls_292",nameB="opls_292"} 55: type[16]={name="opls_140",nameB="opls_140"} 55: type[17]={name="opls_140",nameB="opls_140"} 55: type[18]={name="opls_287",nameB="opls_287"} 55: type[19]={name="opls_290",nameB="opls_290"} 55: type[20]={name="opls_290",nameB="opls_290"} 55: type[21]={name="opls_290",nameB="opls_290"} 55: type[22]={name="opls_235",nameB="opls_235"} 55: type[23]={name="opls_236",nameB="opls_236"} 55: type[24]={name="opls_238",nameB="opls_238"} 55: type[25]={name="opls_241",nameB="opls_241"} 55: type[26]={name="opls_224B",nameB="opls_224B"} 55: type[27]={name="opls_140",nameB="opls_140"} 55: type[28]={name="opls_137",nameB="opls_137"} 55: type[29]={name="opls_140",nameB="opls_140"} 55: type[30]={name="opls_135",nameB="opls_135"} 55: type[31]={name="opls_140",nameB="opls_140"} 55: type[32]={name="opls_140",nameB="opls_140"} 55: type[33]={name="opls_140",nameB="opls_140"} 55: type[34]={name="opls_135",nameB="opls_135"} 55: type[35]={name="opls_140",nameB="opls_140"} 55: type[36]={name="opls_140",nameB="opls_140"} 55: type[37]={name="opls_140",nameB="opls_140"} 55: type[38]={name="opls_235",nameB="opls_235"} 55: type[39]={name="opls_236",nameB="opls_236"} 55: type[40]={name="opls_238",nameB="opls_238"} 55: type[41]={name="opls_241",nameB="opls_241"} 55: type[42]={name="opls_224B",nameB="opls_224B"} 55: type[43]={name="opls_140",nameB="opls_140"} 55: type[44]={name="opls_149",nameB="opls_149"} 55: type[45]={name="opls_140",nameB="opls_140"} 55: type[46]={name="opls_140",nameB="opls_140"} 55: type[47]={name="opls_145",nameB="opls_145"} 55: type[48]={name="opls_145",nameB="opls_145"} 55: type[49]={name="opls_146",nameB="opls_146"} 55: type[50]={name="opls_145",nameB="opls_145"} 55: type[51]={name="opls_146",nameB="opls_146"} 55: type[52]={name="opls_145",nameB="opls_145"} 55: type[53]={name="opls_146",nameB="opls_146"} 55: type[54]={name="opls_145",nameB="opls_145"} 55: type[55]={name="opls_146",nameB="opls_146"} 55: type[56]={name="opls_145",nameB="opls_145"} 55: type[57]={name="opls_146",nameB="opls_146"} 55: type[58]={name="opls_235",nameB="opls_235"} 55: type[59]={name="opls_236",nameB="opls_236"} 55: type[60]={name="opls_238",nameB="opls_238"} 55: type[61]={name="opls_241",nameB="opls_241"} 55: type[62]={name="opls_223B",nameB="opls_223B"} 55: type[63]={name="opls_140",nameB="opls_140"} 55: type[64]={name="opls_140",nameB="opls_140"} 55: type[65]={name="opls_235",nameB="opls_235"} 55: type[66]={name="opls_236",nameB="opls_236"} 55: type[67]={name="opls_238",nameB="opls_238"} 55: type[68]={name="opls_241",nameB="opls_241"} 55: type[69]={name="opls_224B",nameB="opls_224B"} 55: type[70]={name="opls_140",nameB="opls_140"} 55: type[71]={name="opls_136",nameB="opls_136"} 55: type[72]={name="opls_140",nameB="opls_140"} 55: type[73]={name="opls_140",nameB="opls_140"} 55: type[74]={name="opls_308",nameB="opls_308"} 55: type[75]={name="opls_140",nameB="opls_140"} 55: type[76]={name="opls_140",nameB="opls_140"} 55: type[77]={name="opls_307",nameB="opls_307"} 55: type[78]={name="opls_140",nameB="opls_140"} 55: type[79]={name="opls_140",nameB="opls_140"} 55: type[80]={name="opls_303",nameB="opls_303"} 55: type[81]={name="opls_304",nameB="opls_304"} 55: type[82]={name="opls_302",nameB="opls_302"} 55: type[83]={name="opls_300",nameB="opls_300"} 55: type[84]={name="opls_301",nameB="opls_301"} 55: type[85]={name="opls_301",nameB="opls_301"} 55: type[86]={name="opls_300",nameB="opls_300"} 55: type[87]={name="opls_301",nameB="opls_301"} 55: type[88]={name="opls_301",nameB="opls_301"} 55: type[89]={name="opls_235",nameB="opls_235"} 55: type[90]={name="opls_236",nameB="opls_236"} 55: type[91]={name="opls_238",nameB="opls_238"} 55: type[92]={name="opls_241",nameB="opls_241"} 55: type[93]={name="opls_224B",nameB="opls_224B"} 55: type[94]={name="opls_140",nameB="opls_140"} 55: type[95]={name="opls_206",nameB="opls_206"} 55: type[96]={name="opls_140",nameB="opls_140"} 55: type[97]={name="opls_140",nameB="opls_140"} 55: type[98]={name="opls_200",nameB="opls_200"} 55: type[99]={name="opls_204",nameB="opls_204"} 55: type[100]={name="opls_235",nameB="opls_235"} 55: type[101]={name="opls_236",nameB="opls_236"} 55: type[102]={name="opls_238",nameB="opls_238"} 55: type[103]={name="opls_241",nameB="opls_241"} 55: type[104]={name="opls_224B",nameB="opls_224B"} 55: type[105]={name="opls_140",nameB="opls_140"} 55: type[106]={name="opls_136",nameB="opls_136"} 55: type[107]={name="opls_140",nameB="opls_140"} 55: type[108]={name="opls_140",nameB="opls_140"} 55: type[109]={name="opls_274",nameB="opls_274"} 55: type[110]={name="opls_140",nameB="opls_140"} 55: type[111]={name="opls_140",nameB="opls_140"} 55: type[112]={name="opls_271",nameB="opls_271"} 55: type[113]={name="opls_272",nameB="opls_272"} 55: type[114]={name="opls_272",nameB="opls_272"} 55: type[115]={name="opls_235",nameB="opls_235"} 55: type[116]={name="opls_236",nameB="opls_236"} 55: type[117]={name="opls_238",nameB="opls_238"} 55: type[118]={name="opls_241",nameB="opls_241"} 55: type[119]={name="opls_224B",nameB="opls_224B"} 55: type[120]={name="opls_140",nameB="opls_140"} 55: type[121]={name="opls_136",nameB="opls_136"} 55: type[122]={name="opls_140",nameB="opls_140"} 55: type[123]={name="opls_140",nameB="opls_140"} 55: type[124]={name="opls_137",nameB="opls_137"} 55: type[125]={name="opls_140",nameB="opls_140"} 55: type[126]={name="opls_135",nameB="opls_135"} 55: type[127]={name="opls_140",nameB="opls_140"} 55: type[128]={name="opls_140",nameB="opls_140"} 55: type[129]={name="opls_140",nameB="opls_140"} 55: type[130]={name="opls_135",nameB="opls_135"} 55: type[131]={name="opls_140",nameB="opls_140"} 55: type[132]={name="opls_140",nameB="opls_140"} 55: type[133]={name="opls_140",nameB="opls_140"} 55: type[134]={name="opls_235",nameB="opls_235"} 55: type[135]={name="opls_236",nameB="opls_236"} 55: type[136]={name="opls_238",nameB="opls_238"} 55: type[137]={name="opls_241",nameB="opls_241"} 55: type[138]={name="opls_224B",nameB="opls_224B"} 55: type[139]={name="opls_140",nameB="opls_140"} 55: type[140]={name="opls_135",nameB="opls_135"} 55: type[141]={name="opls_140",nameB="opls_140"} 55: type[142]={name="opls_140",nameB="opls_140"} 55: type[143]={name="opls_140",nameB="opls_140"} 55: type[144]={name="opls_235",nameB="opls_235"} 55: type[145]={name="opls_236",nameB="opls_236"} 55: type[146]={name="opls_238",nameB="opls_238"} 55: type[147]={name="opls_241",nameB="opls_241"} 55: type[148]={name="opls_224B",nameB="opls_224B"} 55: type[149]={name="opls_140",nameB="opls_140"} 55: type[150]={name="opls_135",nameB="opls_135"} 55: type[151]={name="opls_140",nameB="opls_140"} 55: type[152]={name="opls_140",nameB="opls_140"} 55: type[153]={name="opls_140",nameB="opls_140"} 55: type[154]={name="opls_235",nameB="opls_235"} 55: type[155]={name="opls_236",nameB="opls_236"} 55: residue (10): 55: residue[0]={name="LYS", nr=1, ic=' '} 55: residue[1]={name="VAL", nr=2, ic=' '} 55: residue[2]={name="PHE", nr=3, ic=' '} 55: residue[3]={name="GLY", nr=4, ic=' '} 55: residue[4]={name="ARG", nr=5, ic=' '} 55: residue[5]={name="CYS", nr=6, ic=' '} 55: residue[6]={name="GLU", nr=7, ic=' '} 55: residue[7]={name="LEU", nr=8, ic=' '} 55: residue[8]={name="ALA", nr=9, ic=' '} 55: residue[9]={name="ALA", nr=10, ic=' '} 55: excls: 55: numLists=156 55: numElements=1828 55: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 55: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 55: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 55: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 55: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 55: 23, 24, 25, 26} 55: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 55: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 55: 14, 15, 22, 23, 24} 55: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 55: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 55: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 55: 16, 17, 18, 22} 55: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 55: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 55: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 55: 17, 18, 19, 20, 21} 55: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 55: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 55: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 55: 20, 21} 55: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 55: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 55: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 55: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 55: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 55: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 55: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 55: 26, 27, 28, 38} 55: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 55: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 55: 30, 34, 38, 39, 40} 55: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 55: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 55: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 55: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 55: 40} 55: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 55: 34, 35, 36, 37, 38, 39, 40} 55: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55: 36, 37, 38} 55: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55: 36, 37, 38} 55: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 55: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 55: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 55: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 55: 36, 37, 38} 55: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 55: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 55: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 55: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 55: 40, 41, 42, 43, 44, 58} 55: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 55: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 55: 45, 46, 47, 58, 59, 60} 55: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 55: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 55: 48, 50, 58, 59, 60, 61, 62} 55: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 55: 60} 55: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55: 50, 51, 52, 54, 58, 59, 60} 55: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 55: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 55: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 55: 52, 53, 54, 55, 56, 58} 55: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 55: 54, 56, 57} 55: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 55: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55: 55, 56, 57} 55: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 55: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 55: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 55: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 55: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 55: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 55: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 55: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 55: 60, 61, 62, 63, 64, 65} 55: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 55: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 55: 65, 66, 67} 55: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 55: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 55: 68, 69} 55: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 55: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 55: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 55: 70, 71, 89} 55: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 55: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 55: 72, 73, 74, 89, 90, 91} 55: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 55: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 55: 75, 76, 77, 89, 90, 91, 92, 93} 55: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 55: 91} 55: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 55: 77, 78, 79, 80, 89, 90, 91} 55: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 55: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 55: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 55: 79, 80, 81, 82, 89} 55: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 55: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 55: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 55: 81, 82, 83, 86} 55: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 55: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 55: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 55: 84, 85, 86, 87, 88} 55: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 55: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 55: 87, 88} 55: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 55: excls[84][num=6]={80, 82, 83, 84, 85, 86} 55: excls[85][num=6]={80, 82, 83, 84, 85, 86} 55: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 55: excls[87][num=6]={80, 82, 83, 86, 87, 88} 55: excls[88][num=6]={80, 82, 83, 86, 87, 88} 55: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 55: 91, 92, 93, 94, 95, 100} 55: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 55: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 55: 96, 97, 98, 100, 101, 102} 55: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 55: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 55: 99, 100, 101, 102, 103, 104} 55: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 55: 102} 55: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 55: 101, 102} 55: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 55: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 55: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 55: excls[99][num=6]={93, 95, 96, 97, 98, 99} 55: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 55: 102, 103, 104, 105, 106, 115} 55: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 55: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 55: 106, 107, 108, 109, 115, 116, 117} 55: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 55: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 55: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 55: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 55: 115, 116, 117} 55: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 55: 110, 111, 112, 113, 114, 115, 116, 117} 55: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 55: 112, 115} 55: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 55: 112, 115} 55: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 55: 112, 113, 114, 115} 55: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 55: 114} 55: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 55: 114} 55: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 55: 114} 55: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 55: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 55: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 55: 115, 116, 117, 118, 119, 120, 121, 134} 55: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 55: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 55: 120, 121, 122, 123, 124, 134, 135, 136} 55: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 55: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 55: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 55: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 55: 134, 135, 136} 55: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 55: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 55: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 55: 130, 134} 55: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 55: 130, 134} 55: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 55: 127, 128, 129, 130, 131, 132, 133, 134} 55: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 55: 129, 130, 131, 132, 133} 55: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 55: 129, 130, 131, 132, 133} 55: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 55: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 55: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 55: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 55: 129, 130, 131, 132, 133} 55: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 55: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 55: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 55: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 55: 134, 135, 136, 137, 138, 139, 140, 144} 55: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 55: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 55: 139, 140, 141, 142, 143, 144, 145, 146} 55: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 55: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 55: 142, 143, 144, 145, 146, 147, 148} 55: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 55: 144, 145, 146} 55: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 55: 144, 145, 146} 55: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 55: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 55: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 55: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 55: 144, 145, 146, 147, 148, 149, 150, 154} 55: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 55: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 55: 149, 150, 151, 152, 153, 154, 155} 55: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 55: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 55: 152, 153, 154, 155} 55: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 55: 154, 155} 55: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 55: 154, 155} 55: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 55: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 55: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 55: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 55: 154, 155} 55: excls[155][num=6]={146, 148, 149, 150, 154, 155} 55: Bond: 55: nr: 468 55: iatoms: 55: 0 type=100 (BONDS) 0 1 55: 1 type=100 (BONDS) 0 2 55: 2 type=100 (BONDS) 0 3 55: 3 type=101 (BONDS) 0 4 55: 4 type=102 (BONDS) 4 5 55: 5 type=103 (BONDS) 4 6 55: 6 type=104 (BONDS) 4 22 55: 7 type=102 (BONDS) 6 7 55: 8 type=102 (BONDS) 6 8 55: 9 type=103 (BONDS) 6 9 55: 10 type=102 (BONDS) 9 10 55: 11 type=102 (BONDS) 9 11 55: 12 type=103 (BONDS) 9 12 55: 13 type=102 (BONDS) 12 13 55: 14 type=102 (BONDS) 12 14 55: 15 type=103 (BONDS) 12 15 55: 16 type=102 (BONDS) 15 16 55: 17 type=102 (BONDS) 15 17 55: 18 type=101 (BONDS) 15 18 55: 19 type=100 (BONDS) 18 19 55: 20 type=100 (BONDS) 18 20 55: 21 type=100 (BONDS) 18 21 55: 22 type=105 (BONDS) 22 23 55: 23 type=106 (BONDS) 22 24 55: 24 type=100 (BONDS) 24 25 55: 25 type=107 (BONDS) 24 26 55: 26 type=102 (BONDS) 26 27 55: 27 type=103 (BONDS) 26 28 55: 28 type=104 (BONDS) 26 38 55: 29 type=102 (BONDS) 28 29 55: 30 type=103 (BONDS) 28 30 55: 31 type=103 (BONDS) 28 34 55: 32 type=102 (BONDS) 30 31 55: 33 type=102 (BONDS) 30 32 55: 34 type=102 (BONDS) 30 33 55: 35 type=102 (BONDS) 34 35 55: 36 type=102 (BONDS) 34 36 55: 37 type=102 (BONDS) 34 37 55: 38 type=105 (BONDS) 38 39 55: 39 type=106 (BONDS) 38 40 55: 40 type=100 (BONDS) 40 41 55: 41 type=107 (BONDS) 40 42 55: 42 type=102 (BONDS) 42 43 55: 43 type=103 (BONDS) 42 44 55: 44 type=104 (BONDS) 42 58 55: 45 type=102 (BONDS) 44 45 55: 46 type=102 (BONDS) 44 46 55: 47 type=108 (BONDS) 44 47 55: 48 type=109 (BONDS) 47 48 55: 49 type=109 (BONDS) 47 50 55: 50 type=110 (BONDS) 48 49 55: 51 type=109 (BONDS) 48 52 55: 52 type=110 (BONDS) 50 51 55: 53 type=109 (BONDS) 50 54 55: 54 type=110 (BONDS) 52 53 55: 55 type=109 (BONDS) 52 56 55: 56 type=110 (BONDS) 54 55 55: 57 type=109 (BONDS) 54 56 55: 58 type=110 (BONDS) 56 57 55: 59 type=105 (BONDS) 58 59 55: 60 type=106 (BONDS) 58 60 55: 61 type=100 (BONDS) 60 61 55: 62 type=107 (BONDS) 60 62 55: 63 type=102 (BONDS) 62 63 55: 64 type=102 (BONDS) 62 64 55: 65 type=104 (BONDS) 62 65 55: 66 type=105 (BONDS) 65 66 55: 67 type=106 (BONDS) 65 67 55: 68 type=100 (BONDS) 67 68 55: 69 type=107 (BONDS) 67 69 55: 70 type=102 (BONDS) 69 70 55: 71 type=103 (BONDS) 69 71 55: 72 type=104 (BONDS) 69 89 55: 73 type=102 (BONDS) 71 72 55: 74 type=102 (BONDS) 71 73 55: 75 type=103 (BONDS) 71 74 55: 76 type=102 (BONDS) 74 75 55: 77 type=102 (BONDS) 74 76 55: 78 type=103 (BONDS) 74 77 55: 79 type=102 (BONDS) 77 78 55: 80 type=102 (BONDS) 77 79 55: 81 type=111 (BONDS) 77 80 55: 82 type=100 (BONDS) 80 81 55: 83 type=112 (BONDS) 80 82 55: 84 type=112 (BONDS) 82 83 55: 85 type=112 (BONDS) 82 86 55: 86 type=100 (BONDS) 83 84 55: 87 type=100 (BONDS) 83 85 55: 88 type=100 (BONDS) 86 87 55: 89 type=100 (BONDS) 86 88 55: 90 type=105 (BONDS) 89 90 55: 91 type=106 (BONDS) 89 91 55: 92 type=100 (BONDS) 91 92 55: 93 type=107 (BONDS) 91 93 55: 94 type=102 (BONDS) 93 94 55: 95 type=103 (BONDS) 93 95 55: 96 type=104 (BONDS) 93 100 55: 97 type=102 (BONDS) 95 96 55: 98 type=102 (BONDS) 95 97 55: 99 type=113 (BONDS) 95 98 55: 100 type=114 (BONDS) 98 99 55: 101 type=105 (BONDS) 100 101 55: 102 type=106 (BONDS) 100 102 55: 103 type=100 (BONDS) 102 103 55: 104 type=107 (BONDS) 102 104 55: 105 type=102 (BONDS) 104 105 55: 106 type=103 (BONDS) 104 106 55: 107 type=104 (BONDS) 104 115 55: 108 type=102 (BONDS) 106 107 55: 109 type=102 (BONDS) 106 108 55: 110 type=103 (BONDS) 106 109 55: 111 type=102 (BONDS) 109 110 55: 112 type=102 (BONDS) 109 111 55: 113 type=104 (BONDS) 109 112 55: 114 type=115 (BONDS) 112 113 55: 115 type=115 (BONDS) 112 114 55: 116 type=105 (BONDS) 115 116 55: 117 type=106 (BONDS) 115 117 55: 118 type=100 (BONDS) 117 118 55: 119 type=107 (BONDS) 117 119 55: 120 type=102 (BONDS) 119 120 55: 121 type=103 (BONDS) 119 121 55: 122 type=104 (BONDS) 119 134 55: 123 type=102 (BONDS) 121 122 55: 124 type=102 (BONDS) 121 123 55: 125 type=103 (BONDS) 121 124 55: 126 type=102 (BONDS) 124 125 55: 127 type=103 (BONDS) 124 126 55: 128 type=103 (BONDS) 124 130 55: 129 type=102 (BONDS) 126 127 55: 130 type=102 (BONDS) 126 128 55: 131 type=102 (BONDS) 126 129 55: 132 type=102 (BONDS) 130 131 55: 133 type=102 (BONDS) 130 132 55: 134 type=102 (BONDS) 130 133 55: 135 type=105 (BONDS) 134 135 55: 136 type=106 (BONDS) 134 136 55: 137 type=100 (BONDS) 136 137 55: 138 type=107 (BONDS) 136 138 55: 139 type=102 (BONDS) 138 139 55: 140 type=103 (BONDS) 138 140 55: 141 type=104 (BONDS) 138 144 55: 142 type=102 (BONDS) 140 141 55: 143 type=102 (BONDS) 140 142 55: 144 type=102 (BONDS) 140 143 55: 145 type=105 (BONDS) 144 145 55: 146 type=106 (BONDS) 144 146 55: 147 type=100 (BONDS) 146 147 55: 148 type=107 (BONDS) 146 148 55: 149 type=102 (BONDS) 148 149 55: 150 type=103 (BONDS) 148 150 55: 151 type=104 (BONDS) 148 154 55: 152 type=102 (BONDS) 150 151 55: 153 type=102 (BONDS) 150 152 55: 154 type=102 (BONDS) 150 153 55: 155 type=105 (BONDS) 154 155 55: G96Bond: 55: nr: 0 55: Morse: 55: nr: 0 55: Cubic Bonds: 55: nr: 0 55: Connect Bonds: 55: nr: 0 55: Harmonic Pot.: 55: nr: 0 55: FENE Bonds: 55: nr: 0 55: Tab. Bonds: 55: nr: 0 55: Tab. Bonds NC: 55: nr: 0 55: Restraint Pot.: 55: nr: 0 55: Angle: 55: nr: 1124 55: iatoms: 55: 0 type=116 (ANGLES) 1 0 2 55: 1 type=116 (ANGLES) 1 0 3 55: 2 type=116 (ANGLES) 1 0 4 55: 3 type=116 (ANGLES) 2 0 3 55: 4 type=116 (ANGLES) 2 0 4 55: 5 type=116 (ANGLES) 3 0 4 55: 6 type=116 (ANGLES) 0 4 5 55: 7 type=117 (ANGLES) 0 4 6 55: 8 type=117 (ANGLES) 0 4 22 55: 9 type=118 (ANGLES) 5 4 6 55: 10 type=116 (ANGLES) 5 4 22 55: 11 type=119 (ANGLES) 6 4 22 55: 12 type=118 (ANGLES) 4 6 7 55: 13 type=118 (ANGLES) 4 6 8 55: 14 type=120 (ANGLES) 4 6 9 55: 15 type=121 (ANGLES) 7 6 8 55: 16 type=118 (ANGLES) 7 6 9 55: 17 type=118 (ANGLES) 8 6 9 55: 18 type=118 (ANGLES) 6 9 10 55: 19 type=118 (ANGLES) 6 9 11 55: 20 type=120 (ANGLES) 6 9 12 55: 21 type=121 (ANGLES) 10 9 11 55: 22 type=118 (ANGLES) 10 9 12 55: 23 type=118 (ANGLES) 11 9 12 55: 24 type=118 (ANGLES) 9 12 13 55: 25 type=118 (ANGLES) 9 12 14 55: 26 type=120 (ANGLES) 9 12 15 55: 27 type=121 (ANGLES) 13 12 14 55: 28 type=118 (ANGLES) 13 12 15 55: 29 type=118 (ANGLES) 14 12 15 55: 30 type=118 (ANGLES) 12 15 16 55: 31 type=118 (ANGLES) 12 15 17 55: 32 type=117 (ANGLES) 12 15 18 55: 33 type=121 (ANGLES) 16 15 17 55: 34 type=116 (ANGLES) 16 15 18 55: 35 type=116 (ANGLES) 17 15 18 55: 36 type=116 (ANGLES) 15 18 19 55: 37 type=116 (ANGLES) 15 18 20 55: 38 type=116 (ANGLES) 15 18 21 55: 39 type=116 (ANGLES) 19 18 20 55: 40 type=116 (ANGLES) 19 18 21 55: 41 type=116 (ANGLES) 20 18 21 55: 42 type=122 (ANGLES) 4 22 23 55: 43 type=123 (ANGLES) 4 22 24 55: 44 type=124 (ANGLES) 23 22 24 55: 45 type=125 (ANGLES) 22 24 25 55: 46 type=126 (ANGLES) 22 24 26 55: 47 type=127 (ANGLES) 25 24 26 55: 48 type=116 (ANGLES) 24 26 27 55: 49 type=128 (ANGLES) 24 26 28 55: 50 type=129 (ANGLES) 24 26 38 55: 51 type=118 (ANGLES) 27 26 28 55: 52 type=116 (ANGLES) 27 26 38 55: 53 type=119 (ANGLES) 28 26 38 55: 54 type=118 (ANGLES) 26 28 29 55: 55 type=120 (ANGLES) 26 28 30 55: 56 type=120 (ANGLES) 26 28 34 55: 57 type=118 (ANGLES) 29 28 30 55: 58 type=118 (ANGLES) 29 28 34 55: 59 type=120 (ANGLES) 30 28 34 55: 60 type=118 (ANGLES) 28 30 31 55: 61 type=118 (ANGLES) 28 30 32 55: 62 type=118 (ANGLES) 28 30 33 55: 63 type=121 (ANGLES) 31 30 32 55: 64 type=121 (ANGLES) 31 30 33 55: 65 type=121 (ANGLES) 32 30 33 55: 66 type=118 (ANGLES) 28 34 35 55: 67 type=118 (ANGLES) 28 34 36 55: 68 type=118 (ANGLES) 28 34 37 55: 69 type=121 (ANGLES) 35 34 36 55: 70 type=121 (ANGLES) 35 34 37 55: 71 type=121 (ANGLES) 36 34 37 55: 72 type=122 (ANGLES) 26 38 39 55: 73 type=123 (ANGLES) 26 38 40 55: 74 type=124 (ANGLES) 39 38 40 55: 75 type=125 (ANGLES) 38 40 41 55: 76 type=126 (ANGLES) 38 40 42 55: 77 type=127 (ANGLES) 41 40 42 55: 78 type=116 (ANGLES) 40 42 43 55: 79 type=128 (ANGLES) 40 42 44 55: 80 type=129 (ANGLES) 40 42 58 55: 81 type=118 (ANGLES) 43 42 44 55: 82 type=116 (ANGLES) 43 42 58 55: 83 type=119 (ANGLES) 44 42 58 55: 84 type=118 (ANGLES) 42 44 45 55: 85 type=118 (ANGLES) 42 44 46 55: 86 type=130 (ANGLES) 42 44 47 55: 87 type=121 (ANGLES) 45 44 46 55: 88 type=116 (ANGLES) 45 44 47 55: 89 type=116 (ANGLES) 46 44 47 55: 90 type=131 (ANGLES) 44 47 48 55: 91 type=131 (ANGLES) 44 47 50 55: 92 type=132 (ANGLES) 48 47 50 55: 93 type=133 (ANGLES) 47 48 49 55: 94 type=132 (ANGLES) 47 48 52 55: 95 type=133 (ANGLES) 49 48 52 55: 96 type=133 (ANGLES) 47 50 51 55: 97 type=132 (ANGLES) 47 50 54 55: 98 type=133 (ANGLES) 51 50 54 55: 99 type=133 (ANGLES) 48 52 53 55: 100 type=132 (ANGLES) 48 52 56 55: 101 type=133 (ANGLES) 53 52 56 55: 102 type=133 (ANGLES) 50 54 55 55: 103 type=132 (ANGLES) 50 54 56 55: 104 type=133 (ANGLES) 55 54 56 55: 105 type=132 (ANGLES) 52 56 54 55: 106 type=133 (ANGLES) 52 56 57 55: 107 type=133 (ANGLES) 54 56 57 55: 108 type=122 (ANGLES) 42 58 59 55: 109 type=123 (ANGLES) 42 58 60 55: 110 type=124 (ANGLES) 59 58 60 55: 111 type=125 (ANGLES) 58 60 61 55: 112 type=126 (ANGLES) 58 60 62 55: 113 type=127 (ANGLES) 61 60 62 55: 114 type=116 (ANGLES) 60 62 63 55: 115 type=116 (ANGLES) 60 62 64 55: 116 type=129 (ANGLES) 60 62 65 55: 117 type=121 (ANGLES) 63 62 64 55: 118 type=116 (ANGLES) 63 62 65 55: 119 type=116 (ANGLES) 64 62 65 55: 120 type=122 (ANGLES) 62 65 66 55: 121 type=123 (ANGLES) 62 65 67 55: 122 type=124 (ANGLES) 66 65 67 55: 123 type=125 (ANGLES) 65 67 68 55: 124 type=126 (ANGLES) 65 67 69 55: 125 type=127 (ANGLES) 68 67 69 55: 126 type=116 (ANGLES) 67 69 70 55: 127 type=128 (ANGLES) 67 69 71 55: 128 type=129 (ANGLES) 67 69 89 55: 129 type=118 (ANGLES) 70 69 71 55: 130 type=116 (ANGLES) 70 69 89 55: 131 type=119 (ANGLES) 71 69 89 55: 132 type=118 (ANGLES) 69 71 72 55: 133 type=118 (ANGLES) 69 71 73 55: 134 type=120 (ANGLES) 69 71 74 55: 135 type=121 (ANGLES) 72 71 73 55: 136 type=118 (ANGLES) 72 71 74 55: 137 type=118 (ANGLES) 73 71 74 55: 138 type=118 (ANGLES) 71 74 75 55: 139 type=118 (ANGLES) 71 74 76 55: 140 type=120 (ANGLES) 71 74 77 55: 141 type=121 (ANGLES) 75 74 76 55: 142 type=118 (ANGLES) 75 74 77 55: 143 type=118 (ANGLES) 76 74 77 55: 144 type=118 (ANGLES) 74 77 78 55: 145 type=118 (ANGLES) 74 77 79 55: 146 type=117 (ANGLES) 74 77 80 55: 147 type=121 (ANGLES) 78 77 79 55: 148 type=116 (ANGLES) 78 77 80 55: 149 type=116 (ANGLES) 79 77 80 55: 150 type=134 (ANGLES) 77 80 81 55: 151 type=135 (ANGLES) 77 80 82 55: 152 type=133 (ANGLES) 81 80 82 55: 153 type=131 (ANGLES) 80 82 83 55: 154 type=131 (ANGLES) 80 82 86 55: 155 type=131 (ANGLES) 83 82 86 55: 156 type=133 (ANGLES) 82 83 84 55: 157 type=133 (ANGLES) 82 83 85 55: 158 type=133 (ANGLES) 84 83 85 55: 159 type=133 (ANGLES) 82 86 87 55: 160 type=133 (ANGLES) 82 86 88 55: 161 type=133 (ANGLES) 87 86 88 55: 162 type=122 (ANGLES) 69 89 90 55: 163 type=123 (ANGLES) 69 89 91 55: 164 type=124 (ANGLES) 90 89 91 55: 165 type=125 (ANGLES) 89 91 92 55: 166 type=126 (ANGLES) 89 91 93 55: 167 type=127 (ANGLES) 92 91 93 55: 168 type=116 (ANGLES) 91 93 94 55: 169 type=128 (ANGLES) 91 93 95 55: 170 type=129 (ANGLES) 91 93 100 55: 171 type=118 (ANGLES) 94 93 95 55: 172 type=116 (ANGLES) 94 93 100 55: 173 type=119 (ANGLES) 95 93 100 55: 174 type=118 (ANGLES) 93 95 96 55: 175 type=118 (ANGLES) 93 95 97 55: 176 type=136 (ANGLES) 93 95 98 55: 177 type=121 (ANGLES) 96 95 97 55: 178 type=116 (ANGLES) 96 95 98 55: 179 type=116 (ANGLES) 97 95 98 55: 180 type=137 (ANGLES) 95 98 99 55: 181 type=122 (ANGLES) 93 100 101 55: 182 type=123 (ANGLES) 93 100 102 55: 183 type=124 (ANGLES) 101 100 102 55: 184 type=125 (ANGLES) 100 102 103 55: 185 type=126 (ANGLES) 100 102 104 55: 186 type=127 (ANGLES) 103 102 104 55: 187 type=116 (ANGLES) 102 104 105 55: 188 type=128 (ANGLES) 102 104 106 55: 189 type=129 (ANGLES) 102 104 115 55: 190 type=118 (ANGLES) 105 104 106 55: 191 type=116 (ANGLES) 105 104 115 55: 192 type=119 (ANGLES) 106 104 115 55: 193 type=118 (ANGLES) 104 106 107 55: 194 type=118 (ANGLES) 104 106 108 55: 195 type=120 (ANGLES) 104 106 109 55: 196 type=121 (ANGLES) 107 106 108 55: 197 type=118 (ANGLES) 107 106 109 55: 198 type=118 (ANGLES) 108 106 109 55: 199 type=118 (ANGLES) 106 109 110 55: 200 type=118 (ANGLES) 106 109 111 55: 201 type=119 (ANGLES) 106 109 112 55: 202 type=121 (ANGLES) 110 109 111 55: 203 type=116 (ANGLES) 110 109 112 55: 204 type=116 (ANGLES) 111 109 112 55: 205 type=138 (ANGLES) 109 112 113 55: 206 type=138 (ANGLES) 109 112 114 55: 207 type=139 (ANGLES) 113 112 114 55: 208 type=122 (ANGLES) 104 115 116 55: 209 type=123 (ANGLES) 104 115 117 55: 210 type=124 (ANGLES) 116 115 117 55: 211 type=125 (ANGLES) 115 117 118 55: 212 type=126 (ANGLES) 115 117 119 55: 213 type=127 (ANGLES) 118 117 119 55: 214 type=116 (ANGLES) 117 119 120 55: 215 type=128 (ANGLES) 117 119 121 55: 216 type=129 (ANGLES) 117 119 134 55: 217 type=118 (ANGLES) 120 119 121 55: 218 type=116 (ANGLES) 120 119 134 55: 219 type=119 (ANGLES) 121 119 134 55: 220 type=118 (ANGLES) 119 121 122 55: 221 type=118 (ANGLES) 119 121 123 55: 222 type=120 (ANGLES) 119 121 124 55: 223 type=121 (ANGLES) 122 121 123 55: 224 type=118 (ANGLES) 122 121 124 55: 225 type=118 (ANGLES) 123 121 124 55: 226 type=118 (ANGLES) 121 124 125 55: 227 type=120 (ANGLES) 121 124 126 55: 228 type=120 (ANGLES) 121 124 130 55: 229 type=118 (ANGLES) 125 124 126 55: 230 type=118 (ANGLES) 125 124 130 55: 231 type=120 (ANGLES) 126 124 130 55: 232 type=118 (ANGLES) 124 126 127 55: 233 type=118 (ANGLES) 124 126 128 55: 234 type=118 (ANGLES) 124 126 129 55: 235 type=121 (ANGLES) 127 126 128 55: 236 type=121 (ANGLES) 127 126 129 55: 237 type=121 (ANGLES) 128 126 129 55: 238 type=118 (ANGLES) 124 130 131 55: 239 type=118 (ANGLES) 124 130 132 55: 240 type=118 (ANGLES) 124 130 133 55: 241 type=121 (ANGLES) 131 130 132 55: 242 type=121 (ANGLES) 131 130 133 55: 243 type=121 (ANGLES) 132 130 133 55: 244 type=122 (ANGLES) 119 134 135 55: 245 type=123 (ANGLES) 119 134 136 55: 246 type=124 (ANGLES) 135 134 136 55: 247 type=125 (ANGLES) 134 136 137 55: 248 type=126 (ANGLES) 134 136 138 55: 249 type=127 (ANGLES) 137 136 138 55: 250 type=116 (ANGLES) 136 138 139 55: 251 type=128 (ANGLES) 136 138 140 55: 252 type=129 (ANGLES) 136 138 144 55: 253 type=118 (ANGLES) 139 138 140 55: 254 type=116 (ANGLES) 139 138 144 55: 255 type=119 (ANGLES) 140 138 144 55: 256 type=118 (ANGLES) 138 140 141 55: 257 type=118 (ANGLES) 138 140 142 55: 258 type=118 (ANGLES) 138 140 143 55: 259 type=121 (ANGLES) 141 140 142 55: 260 type=121 (ANGLES) 141 140 143 55: 261 type=121 (ANGLES) 142 140 143 55: 262 type=122 (ANGLES) 138 144 145 55: 263 type=123 (ANGLES) 138 144 146 55: 264 type=124 (ANGLES) 145 144 146 55: 265 type=125 (ANGLES) 144 146 147 55: 266 type=126 (ANGLES) 144 146 148 55: 267 type=127 (ANGLES) 147 146 148 55: 268 type=116 (ANGLES) 146 148 149 55: 269 type=128 (ANGLES) 146 148 150 55: 270 type=129 (ANGLES) 146 148 154 55: 271 type=118 (ANGLES) 149 148 150 55: 272 type=116 (ANGLES) 149 148 154 55: 273 type=119 (ANGLES) 150 148 154 55: 274 type=118 (ANGLES) 148 150 151 55: 275 type=118 (ANGLES) 148 150 152 55: 276 type=118 (ANGLES) 148 150 153 55: 277 type=121 (ANGLES) 151 150 152 55: 278 type=121 (ANGLES) 151 150 153 55: 279 type=121 (ANGLES) 152 150 153 55: 280 type=122 (ANGLES) 148 154 155 55: G96Angle: 55: nr: 0 55: Restr. Angles: 55: nr: 0 55: Lin. Angle: 55: nr: 0 55: Bond-Cross: 55: nr: 0 55: BA-Cross: 55: nr: 0 55: U-B: 55: nr: 0 55: Quartic Angles: 55: nr: 0 55: Tab. Angles: 55: nr: 0 55: Proper Dih.: 55: nr: 145 55: iatoms: 55: 0 type=140 (PDIHS) 4 24 22 23 55: 1 type=141 (PDIHS) 22 26 24 25 55: 2 type=140 (PDIHS) 26 40 38 39 55: 3 type=141 (PDIHS) 38 42 40 41 55: 4 type=140 (PDIHS) 42 60 58 59 55: 5 type=142 (PDIHS) 44 47 50 48 55: 6 type=142 (PDIHS) 47 52 48 49 55: 7 type=142 (PDIHS) 47 54 50 51 55: 8 type=142 (PDIHS) 48 56 52 53 55: 9 type=142 (PDIHS) 50 56 54 55 55: 10 type=142 (PDIHS) 52 54 56 57 55: 11 type=141 (PDIHS) 58 62 60 61 55: 12 type=140 (PDIHS) 62 67 65 66 55: 13 type=141 (PDIHS) 65 69 67 68 55: 14 type=140 (PDIHS) 69 91 89 90 55: 15 type=141 (PDIHS) 77 82 80 81 55: 16 type=140 (PDIHS) 80 83 82 86 55: 17 type=141 (PDIHS) 82 84 83 85 55: 18 type=141 (PDIHS) 82 87 86 88 55: 19 type=141 (PDIHS) 89 93 91 92 55: 20 type=140 (PDIHS) 93 102 100 101 55: 21 type=141 (PDIHS) 100 104 102 103 55: 22 type=140 (PDIHS) 104 117 115 116 55: 23 type=140 (PDIHS) 109 113 112 114 55: 24 type=141 (PDIHS) 115 119 117 118 55: 25 type=140 (PDIHS) 119 136 134 135 55: 26 type=141 (PDIHS) 134 138 136 137 55: 27 type=140 (PDIHS) 138 146 144 145 55: 28 type=141 (PDIHS) 144 148 146 147 55: Ryckaert-Bell.: 55: nr: 1565 55: iatoms: 55: 0 type=143 (RBDIHS) 1 0 4 5 55: 1 type=144 (RBDIHS) 1 0 4 6 55: 2 type=144 (RBDIHS) 1 0 4 22 55: 3 type=143 (RBDIHS) 2 0 4 5 55: 4 type=144 (RBDIHS) 2 0 4 6 55: 5 type=144 (RBDIHS) 2 0 4 22 55: 6 type=143 (RBDIHS) 3 0 4 5 55: 7 type=144 (RBDIHS) 3 0 4 6 55: 8 type=144 (RBDIHS) 3 0 4 22 55: 9 type=145 (RBDIHS) 0 4 6 9 55: 10 type=146 (RBDIHS) 22 4 6 9 55: 11 type=147 (RBDIHS) 0 4 6 7 55: 12 type=147 (RBDIHS) 0 4 6 8 55: 13 type=148 (RBDIHS) 5 4 6 7 55: 14 type=148 (RBDIHS) 5 4 6 8 55: 15 type=148 (RBDIHS) 5 4 6 9 55: 16 type=149 (RBDIHS) 22 4 6 7 55: 17 type=149 (RBDIHS) 22 4 6 8 55: 18 type=150 (RBDIHS) 0 4 22 24 55: 19 type=151 (RBDIHS) 6 4 22 24 55: 20 type=148 (RBDIHS) 4 6 9 10 55: 21 type=148 (RBDIHS) 4 6 9 11 55: 22 type=152 (RBDIHS) 4 6 9 12 55: 23 type=148 (RBDIHS) 7 6 9 10 55: 24 type=148 (RBDIHS) 7 6 9 11 55: 25 type=148 (RBDIHS) 7 6 9 12 55: 26 type=148 (RBDIHS) 8 6 9 10 55: 27 type=148 (RBDIHS) 8 6 9 11 55: 28 type=148 (RBDIHS) 8 6 9 12 55: 29 type=148 (RBDIHS) 6 9 12 13 55: 30 type=148 (RBDIHS) 6 9 12 14 55: 31 type=152 (RBDIHS) 6 9 12 15 55: 32 type=148 (RBDIHS) 10 9 12 13 55: 33 type=148 (RBDIHS) 10 9 12 14 55: 34 type=148 (RBDIHS) 10 9 12 15 55: 35 type=148 (RBDIHS) 11 9 12 13 55: 36 type=148 (RBDIHS) 11 9 12 14 55: 37 type=148 (RBDIHS) 11 9 12 15 55: 38 type=148 (RBDIHS) 9 12 15 16 55: 39 type=148 (RBDIHS) 9 12 15 17 55: 40 type=153 (RBDIHS) 9 12 15 18 55: 41 type=148 (RBDIHS) 13 12 15 16 55: 42 type=148 (RBDIHS) 13 12 15 17 55: 43 type=154 (RBDIHS) 13 12 15 18 55: 44 type=148 (RBDIHS) 14 12 15 16 55: 45 type=148 (RBDIHS) 14 12 15 17 55: 46 type=154 (RBDIHS) 14 12 15 18 55: 47 type=144 (RBDIHS) 12 15 18 19 55: 48 type=144 (RBDIHS) 12 15 18 20 55: 49 type=144 (RBDIHS) 12 15 18 21 55: 50 type=143 (RBDIHS) 16 15 18 19 55: 51 type=143 (RBDIHS) 16 15 18 20 55: 52 type=143 (RBDIHS) 16 15 18 21 55: 53 type=143 (RBDIHS) 17 15 18 19 55: 54 type=143 (RBDIHS) 17 15 18 20 55: 55 type=143 (RBDIHS) 17 15 18 21 55: 56 type=155 (RBDIHS) 4 22 24 25 55: 57 type=156 (RBDIHS) 4 22 24 26 55: 58 type=155 (RBDIHS) 23 22 24 25 55: 59 type=157 (RBDIHS) 23 22 24 26 55: 60 type=158 (RBDIHS) 22 24 26 28 55: 61 type=159 (RBDIHS) 22 24 26 38 55: 62 type=160 (RBDIHS) 24 26 28 30 55: 63 type=160 (RBDIHS) 24 26 28 34 55: 64 type=161 (RBDIHS) 38 26 28 30 55: 65 type=161 (RBDIHS) 38 26 28 34 55: 66 type=147 (RBDIHS) 24 26 28 29 55: 67 type=148 (RBDIHS) 27 26 28 29 55: 68 type=148 (RBDIHS) 27 26 28 30 55: 69 type=148 (RBDIHS) 27 26 28 34 55: 70 type=149 (RBDIHS) 38 26 28 29 55: 71 type=150 (RBDIHS) 24 26 38 40 55: 72 type=151 (RBDIHS) 28 26 38 40 55: 73 type=148 (RBDIHS) 26 28 30 31 55: 74 type=148 (RBDIHS) 26 28 30 32 55: 75 type=148 (RBDIHS) 26 28 30 33 55: 76 type=148 (RBDIHS) 29 28 30 31 55: 77 type=148 (RBDIHS) 29 28 30 32 55: 78 type=148 (RBDIHS) 29 28 30 33 55: 79 type=148 (RBDIHS) 34 28 30 31 55: 80 type=148 (RBDIHS) 34 28 30 32 55: 81 type=148 (RBDIHS) 34 28 30 33 55: 82 type=148 (RBDIHS) 26 28 34 35 55: 83 type=148 (RBDIHS) 26 28 34 36 55: 84 type=148 (RBDIHS) 26 28 34 37 55: 85 type=148 (RBDIHS) 29 28 34 35 55: 86 type=148 (RBDIHS) 29 28 34 36 55: 87 type=148 (RBDIHS) 29 28 34 37 55: 88 type=148 (RBDIHS) 30 28 34 35 55: 89 type=148 (RBDIHS) 30 28 34 36 55: 90 type=148 (RBDIHS) 30 28 34 37 55: 91 type=155 (RBDIHS) 26 38 40 41 55: 92 type=156 (RBDIHS) 26 38 40 42 55: 93 type=155 (RBDIHS) 39 38 40 41 55: 94 type=157 (RBDIHS) 39 38 40 42 55: 95 type=158 (RBDIHS) 38 40 42 44 55: 96 type=159 (RBDIHS) 38 40 42 58 55: 97 type=147 (RBDIHS) 40 42 44 45 55: 98 type=147 (RBDIHS) 40 42 44 46 55: 99 type=162 (RBDIHS) 40 42 44 47 55: 100 type=148 (RBDIHS) 43 42 44 45 55: 101 type=148 (RBDIHS) 43 42 44 46 55: 102 type=163 (RBDIHS) 43 42 44 47 55: 103 type=149 (RBDIHS) 58 42 44 45 55: 104 type=149 (RBDIHS) 58 42 44 46 55: 105 type=164 (RBDIHS) 58 42 44 47 55: 106 type=150 (RBDIHS) 40 42 58 60 55: 107 type=151 (RBDIHS) 44 42 58 60 55: 108 type=165 (RBDIHS) 44 47 48 49 55: 109 type=165 (RBDIHS) 44 47 48 52 55: 110 type=165 (RBDIHS) 50 47 48 49 55: 111 type=165 (RBDIHS) 50 47 48 52 55: 112 type=165 (RBDIHS) 44 47 50 51 55: 113 type=165 (RBDIHS) 44 47 50 54 55: 114 type=165 (RBDIHS) 48 47 50 51 55: 115 type=165 (RBDIHS) 48 47 50 54 55: 116 type=165 (RBDIHS) 47 48 52 53 55: 117 type=165 (RBDIHS) 47 48 52 56 55: 118 type=165 (RBDIHS) 49 48 52 53 55: 119 type=165 (RBDIHS) 49 48 52 56 55: 120 type=165 (RBDIHS) 47 50 54 55 55: 121 type=165 (RBDIHS) 47 50 54 56 55: 122 type=165 (RBDIHS) 51 50 54 55 55: 123 type=165 (RBDIHS) 51 50 54 56 55: 124 type=165 (RBDIHS) 48 52 56 54 55: 125 type=165 (RBDIHS) 48 52 56 57 55: 126 type=165 (RBDIHS) 53 52 56 54 55: 127 type=165 (RBDIHS) 53 52 56 57 55: 128 type=165 (RBDIHS) 50 54 56 52 55: 129 type=165 (RBDIHS) 50 54 56 57 55: 130 type=165 (RBDIHS) 55 54 56 52 55: 131 type=165 (RBDIHS) 55 54 56 57 55: 132 type=155 (RBDIHS) 42 58 60 61 55: 133 type=156 (RBDIHS) 42 58 60 62 55: 134 type=155 (RBDIHS) 59 58 60 61 55: 135 type=157 (RBDIHS) 59 58 60 62 55: 136 type=159 (RBDIHS) 58 60 62 65 55: 137 type=150 (RBDIHS) 60 62 65 67 55: 138 type=155 (RBDIHS) 62 65 67 68 55: 139 type=156 (RBDIHS) 62 65 67 69 55: 140 type=155 (RBDIHS) 66 65 67 68 55: 141 type=157 (RBDIHS) 66 65 67 69 55: 142 type=158 (RBDIHS) 65 67 69 71 55: 143 type=159 (RBDIHS) 65 67 69 89 55: 144 type=166 (RBDIHS) 67 69 71 74 55: 145 type=167 (RBDIHS) 89 69 71 74 55: 146 type=147 (RBDIHS) 67 69 71 72 55: 147 type=147 (RBDIHS) 67 69 71 73 55: 148 type=148 (RBDIHS) 70 69 71 72 55: 149 type=148 (RBDIHS) 70 69 71 73 55: 150 type=148 (RBDIHS) 70 69 71 74 55: 151 type=149 (RBDIHS) 89 69 71 72 55: 152 type=149 (RBDIHS) 89 69 71 73 55: 153 type=150 (RBDIHS) 67 69 89 91 55: 154 type=151 (RBDIHS) 71 69 89 91 55: 155 type=148 (RBDIHS) 69 71 74 75 55: 156 type=148 (RBDIHS) 69 71 74 76 55: 157 type=152 (RBDIHS) 69 71 74 77 55: 158 type=148 (RBDIHS) 72 71 74 75 55: 159 type=148 (RBDIHS) 72 71 74 76 55: 160 type=148 (RBDIHS) 72 71 74 77 55: 161 type=148 (RBDIHS) 73 71 74 75 55: 162 type=148 (RBDIHS) 73 71 74 76 55: 163 type=148 (RBDIHS) 73 71 74 77 55: 164 type=148 (RBDIHS) 71 74 77 78 55: 165 type=148 (RBDIHS) 71 74 77 79 55: 166 type=153 (RBDIHS) 71 74 77 80 55: 167 type=148 (RBDIHS) 75 74 77 78 55: 168 type=148 (RBDIHS) 75 74 77 79 55: 169 type=168 (RBDIHS) 75 74 77 80 55: 170 type=148 (RBDIHS) 76 74 77 78 55: 171 type=148 (RBDIHS) 76 74 77 79 55: 172 type=168 (RBDIHS) 76 74 77 80 55: 173 type=169 (RBDIHS) 74 77 80 81 55: 174 type=170 (RBDIHS) 74 77 80 82 55: 175 type=171 (RBDIHS) 78 77 80 82 55: 176 type=171 (RBDIHS) 79 77 80 82 55: 177 type=172 (RBDIHS) 77 80 82 83 55: 178 type=172 (RBDIHS) 77 80 82 86 55: 179 type=173 (RBDIHS) 81 80 82 83 55: 180 type=173 (RBDIHS) 81 80 82 86 55: 181 type=173 (RBDIHS) 80 82 83 84 55: 182 type=173 (RBDIHS) 80 82 83 85 55: 183 type=173 (RBDIHS) 86 82 83 84 55: 184 type=173 (RBDIHS) 86 82 83 85 55: 185 type=173 (RBDIHS) 80 82 86 87 55: 186 type=173 (RBDIHS) 80 82 86 88 55: 187 type=173 (RBDIHS) 83 82 86 87 55: 188 type=173 (RBDIHS) 83 82 86 88 55: 189 type=155 (RBDIHS) 69 89 91 92 55: 190 type=156 (RBDIHS) 69 89 91 93 55: 191 type=155 (RBDIHS) 90 89 91 92 55: 192 type=157 (RBDIHS) 90 89 91 93 55: 193 type=158 (RBDIHS) 89 91 93 95 55: 194 type=159 (RBDIHS) 89 91 93 100 55: 195 type=174 (RBDIHS) 91 93 95 98 55: 196 type=175 (RBDIHS) 100 93 95 98 55: 197 type=147 (RBDIHS) 91 93 95 96 55: 198 type=147 (RBDIHS) 91 93 95 97 55: 199 type=148 (RBDIHS) 94 93 95 96 55: 200 type=148 (RBDIHS) 94 93 95 97 55: 201 type=176 (RBDIHS) 94 93 95 98 55: 202 type=149 (RBDIHS) 100 93 95 96 55: 203 type=149 (RBDIHS) 100 93 95 97 55: 204 type=150 (RBDIHS) 91 93 100 102 55: 205 type=151 (RBDIHS) 95 93 100 102 55: 206 type=177 (RBDIHS) 93 95 98 99 55: 207 type=178 (RBDIHS) 96 95 98 99 55: 208 type=178 (RBDIHS) 97 95 98 99 55: 209 type=155 (RBDIHS) 93 100 102 103 55: 210 type=156 (RBDIHS) 93 100 102 104 55: 211 type=155 (RBDIHS) 101 100 102 103 55: 212 type=157 (RBDIHS) 101 100 102 104 55: 213 type=158 (RBDIHS) 100 102 104 106 55: 214 type=159 (RBDIHS) 100 102 104 115 55: 215 type=179 (RBDIHS) 102 104 106 109 55: 216 type=180 (RBDIHS) 115 104 106 109 55: 217 type=147 (RBDIHS) 102 104 106 107 55: 218 type=147 (RBDIHS) 102 104 106 108 55: 219 type=148 (RBDIHS) 105 104 106 107 55: 220 type=148 (RBDIHS) 105 104 106 108 55: 221 type=148 (RBDIHS) 105 104 106 109 55: 222 type=149 (RBDIHS) 115 104 106 107 55: 223 type=149 (RBDIHS) 115 104 106 108 55: 224 type=150 (RBDIHS) 102 104 115 117 55: 225 type=151 (RBDIHS) 106 104 115 117 55: 226 type=148 (RBDIHS) 104 106 109 110 55: 227 type=148 (RBDIHS) 104 106 109 111 55: 228 type=181 (RBDIHS) 104 106 109 112 55: 229 type=148 (RBDIHS) 107 106 109 110 55: 230 type=148 (RBDIHS) 107 106 109 111 55: 231 type=182 (RBDIHS) 107 106 109 112 55: 232 type=148 (RBDIHS) 108 106 109 110 55: 233 type=148 (RBDIHS) 108 106 109 111 55: 234 type=182 (RBDIHS) 108 106 109 112 55: 235 type=183 (RBDIHS) 106 109 112 113 55: 236 type=183 (RBDIHS) 106 109 112 114 55: 237 type=155 (RBDIHS) 104 115 117 118 55: 238 type=156 (RBDIHS) 104 115 117 119 55: 239 type=155 (RBDIHS) 116 115 117 118 55: 240 type=157 (RBDIHS) 116 115 117 119 55: 241 type=158 (RBDIHS) 115 117 119 121 55: 242 type=159 (RBDIHS) 115 117 119 134 55: 243 type=184 (RBDIHS) 117 119 121 124 55: 244 type=185 (RBDIHS) 134 119 121 124 55: 245 type=147 (RBDIHS) 117 119 121 122 55: 246 type=147 (RBDIHS) 117 119 121 123 55: 247 type=148 (RBDIHS) 120 119 121 122 55: 248 type=148 (RBDIHS) 120 119 121 123 55: 249 type=148 (RBDIHS) 120 119 121 124 55: 250 type=149 (RBDIHS) 134 119 121 122 55: 251 type=149 (RBDIHS) 134 119 121 123 55: 252 type=150 (RBDIHS) 117 119 134 136 55: 253 type=151 (RBDIHS) 121 119 134 136 55: 254 type=148 (RBDIHS) 119 121 124 125 55: 255 type=152 (RBDIHS) 119 121 124 126 55: 256 type=152 (RBDIHS) 119 121 124 130 55: 257 type=148 (RBDIHS) 122 121 124 125 55: 258 type=148 (RBDIHS) 122 121 124 126 55: 259 type=148 (RBDIHS) 122 121 124 130 55: 260 type=148 (RBDIHS) 123 121 124 125 55: 261 type=148 (RBDIHS) 123 121 124 126 55: 262 type=148 (RBDIHS) 123 121 124 130 55: 263 type=148 (RBDIHS) 121 124 126 127 55: 264 type=148 (RBDIHS) 121 124 126 128 55: 265 type=148 (RBDIHS) 121 124 126 129 55: 266 type=148 (RBDIHS) 125 124 126 127 55: 267 type=148 (RBDIHS) 125 124 126 128 55: 268 type=148 (RBDIHS) 125 124 126 129 55: 269 type=148 (RBDIHS) 130 124 126 127 55: 270 type=148 (RBDIHS) 130 124 126 128 55: 271 type=148 (RBDIHS) 130 124 126 129 55: 272 type=148 (RBDIHS) 121 124 130 131 55: 273 type=148 (RBDIHS) 121 124 130 132 55: 274 type=148 (RBDIHS) 121 124 130 133 55: 275 type=148 (RBDIHS) 125 124 130 131 55: 276 type=148 (RBDIHS) 125 124 130 132 55: 277 type=148 (RBDIHS) 125 124 130 133 55: 278 type=148 (RBDIHS) 126 124 130 131 55: 279 type=148 (RBDIHS) 126 124 130 132 55: 280 type=148 (RBDIHS) 126 124 130 133 55: 281 type=155 (RBDIHS) 119 134 136 137 55: 282 type=156 (RBDIHS) 119 134 136 138 55: 283 type=155 (RBDIHS) 135 134 136 137 55: 284 type=157 (RBDIHS) 135 134 136 138 55: 285 type=158 (RBDIHS) 134 136 138 140 55: 286 type=159 (RBDIHS) 134 136 138 144 55: 287 type=147 (RBDIHS) 136 138 140 141 55: 288 type=147 (RBDIHS) 136 138 140 142 55: 289 type=147 (RBDIHS) 136 138 140 143 55: 290 type=148 (RBDIHS) 139 138 140 141 55: 291 type=148 (RBDIHS) 139 138 140 142 55: 292 type=148 (RBDIHS) 139 138 140 143 55: 293 type=149 (RBDIHS) 144 138 140 141 55: 294 type=149 (RBDIHS) 144 138 140 142 55: 295 type=149 (RBDIHS) 144 138 140 143 55: 296 type=150 (RBDIHS) 136 138 144 146 55: 297 type=151 (RBDIHS) 140 138 144 146 55: 298 type=155 (RBDIHS) 138 144 146 147 55: 299 type=156 (RBDIHS) 138 144 146 148 55: 300 type=155 (RBDIHS) 145 144 146 147 55: 301 type=157 (RBDIHS) 145 144 146 148 55: 302 type=158 (RBDIHS) 144 146 148 150 55: 303 type=159 (RBDIHS) 144 146 148 154 55: 304 type=147 (RBDIHS) 146 148 150 151 55: 305 type=147 (RBDIHS) 146 148 150 152 55: 306 type=147 (RBDIHS) 146 148 150 153 55: 307 type=148 (RBDIHS) 149 148 150 151 55: 308 type=148 (RBDIHS) 149 148 150 152 55: 309 type=148 (RBDIHS) 149 148 150 153 55: 310 type=149 (RBDIHS) 154 148 150 151 55: 311 type=149 (RBDIHS) 154 148 150 152 55: 312 type=149 (RBDIHS) 154 148 150 153 55: Restr. Dih.: 55: nr: 0 55: CBT Dih.: 55: nr: 0 55: Fourier Dih.: 55: nr: 0 55: Improper Dih.: 55: nr: 0 55: Per. Imp. Dih.: 55: nr: 0 55: Tab. Dih.: 55: nr: 0 55: CMAP Dih.: 55: nr: 0 55: GB 1-2 Pol. (unused): 55: nr: 0 55: GB 1-3 Pol. (unused): 55: nr: 0 55: GB 1-4 Pol. (unused): 55: nr: 0 55: GB Polarization (unused): 55: nr: 0 55: Nonpolar Sol. (unused): 55: nr: 0 55: LJ-14: 55: nr: 1197 55: iatoms: 55: 0 type=186 (LJ14) 0 7 55: 1 type=186 (LJ14) 0 8 55: 2 type=187 (LJ14) 0 9 55: 3 type=188 (LJ14) 0 23 55: 4 type=189 (LJ14) 0 24 55: 5 type=190 (LJ14) 1 5 55: 6 type=190 (LJ14) 1 6 55: 7 type=190 (LJ14) 1 22 55: 8 type=190 (LJ14) 2 5 55: 9 type=190 (LJ14) 2 6 55: 10 type=190 (LJ14) 2 22 55: 11 type=190 (LJ14) 3 5 55: 12 type=190 (LJ14) 3 6 55: 13 type=190 (LJ14) 3 22 55: 14 type=191 (LJ14) 4 10 55: 15 type=191 (LJ14) 4 11 55: 16 type=192 (LJ14) 4 12 55: 17 type=190 (LJ14) 4 25 55: 18 type=192 (LJ14) 4 26 55: 19 type=193 (LJ14) 5 7 55: 20 type=193 (LJ14) 5 8 55: 21 type=191 (LJ14) 5 9 55: 22 type=194 (LJ14) 5 23 55: 23 type=186 (LJ14) 5 24 55: 24 type=191 (LJ14) 6 13 55: 25 type=191 (LJ14) 6 14 55: 26 type=192 (LJ14) 6 15 55: 27 type=195 (LJ14) 6 23 55: 28 type=187 (LJ14) 6 24 55: 29 type=193 (LJ14) 7 10 55: 30 type=193 (LJ14) 7 11 55: 31 type=191 (LJ14) 7 12 55: 32 type=196 (LJ14) 7 22 55: 33 type=193 (LJ14) 8 10 55: 34 type=193 (LJ14) 8 11 55: 35 type=191 (LJ14) 8 12 55: 36 type=196 (LJ14) 8 22 55: 37 type=191 (LJ14) 9 16 55: 38 type=191 (LJ14) 9 17 55: 39 type=187 (LJ14) 9 18 55: 40 type=197 (LJ14) 9 22 55: 41 type=193 (LJ14) 10 13 55: 42 type=193 (LJ14) 10 14 55: 43 type=191 (LJ14) 10 15 55: 44 type=193 (LJ14) 11 13 55: 45 type=193 (LJ14) 11 14 55: 46 type=191 (LJ14) 11 15 55: 47 type=190 (LJ14) 12 19 55: 48 type=190 (LJ14) 12 20 55: 49 type=190 (LJ14) 12 21 55: 50 type=193 (LJ14) 13 16 55: 51 type=193 (LJ14) 13 17 55: 52 type=186 (LJ14) 13 18 55: 53 type=193 (LJ14) 14 16 55: 54 type=193 (LJ14) 14 17 55: 55 type=186 (LJ14) 14 18 55: 56 type=190 (LJ14) 16 19 55: 57 type=190 (LJ14) 16 20 55: 58 type=190 (LJ14) 16 21 55: 59 type=190 (LJ14) 17 19 55: 60 type=190 (LJ14) 17 20 55: 61 type=190 (LJ14) 17 21 55: 62 type=196 (LJ14) 22 27 55: 63 type=197 (LJ14) 22 28 55: 64 type=198 (LJ14) 22 38 55: 65 type=190 (LJ14) 23 25 55: 66 type=195 (LJ14) 23 26 55: 67 type=186 (LJ14) 24 29 55: 68 type=187 (LJ14) 24 30 55: 69 type=187 (LJ14) 24 34 55: 70 type=188 (LJ14) 24 39 55: 71 type=189 (LJ14) 24 40 55: 72 type=190 (LJ14) 25 27 55: 73 type=190 (LJ14) 25 28 55: 74 type=190 (LJ14) 25 38 55: 75 type=191 (LJ14) 26 31 55: 76 type=191 (LJ14) 26 32 55: 77 type=191 (LJ14) 26 33 55: 78 type=191 (LJ14) 26 35 55: 79 type=191 (LJ14) 26 36 55: 80 type=191 (LJ14) 26 37 55: 81 type=190 (LJ14) 26 41 55: 82 type=192 (LJ14) 26 42 55: 83 type=193 (LJ14) 27 29 55: 84 type=191 (LJ14) 27 30 55: 85 type=191 (LJ14) 27 34 55: 86 type=194 (LJ14) 27 39 55: 87 type=186 (LJ14) 27 40 55: 88 type=195 (LJ14) 28 39 55: 89 type=187 (LJ14) 28 40 55: 90 type=193 (LJ14) 29 31 55: 91 type=193 (LJ14) 29 32 55: 92 type=193 (LJ14) 29 33 55: 93 type=193 (LJ14) 29 35 55: 94 type=193 (LJ14) 29 36 55: 95 type=193 (LJ14) 29 37 55: 96 type=196 (LJ14) 29 38 55: 97 type=191 (LJ14) 30 35 55: 98 type=191 (LJ14) 30 36 55: 99 type=191 (LJ14) 30 37 55: 100 type=197 (LJ14) 30 38 55: 101 type=191 (LJ14) 31 34 55: 102 type=191 (LJ14) 32 34 55: 103 type=191 (LJ14) 33 34 55: 104 type=197 (LJ14) 34 38 55: 105 type=196 (LJ14) 38 43 55: 106 type=197 (LJ14) 38 44 55: 107 type=198 (LJ14) 38 58 55: 108 type=190 (LJ14) 39 41 55: 109 type=195 (LJ14) 39 42 55: 110 type=186 (LJ14) 40 45 55: 111 type=186 (LJ14) 40 46 55: 112 type=199 (LJ14) 40 47 55: 113 type=188 (LJ14) 40 59 55: 114 type=189 (LJ14) 40 60 55: 115 type=190 (LJ14) 41 43 55: 116 type=190 (LJ14) 41 44 55: 117 type=190 (LJ14) 41 58 55: 118 type=200 (LJ14) 42 48 55: 119 type=200 (LJ14) 42 50 55: 120 type=190 (LJ14) 42 61 55: 121 type=192 (LJ14) 42 62 55: 122 type=193 (LJ14) 43 45 55: 123 type=193 (LJ14) 43 46 55: 124 type=201 (LJ14) 43 47 55: 125 type=194 (LJ14) 43 59 55: 126 type=186 (LJ14) 43 60 55: 127 type=202 (LJ14) 44 49 55: 128 type=202 (LJ14) 44 51 55: 129 type=200 (LJ14) 44 52 55: 130 type=200 (LJ14) 44 54 55: 131 type=195 (LJ14) 44 59 55: 132 type=187 (LJ14) 44 60 55: 133 type=201 (LJ14) 45 48 55: 134 type=201 (LJ14) 45 50 55: 135 type=196 (LJ14) 45 58 55: 136 type=201 (LJ14) 46 48 55: 137 type=201 (LJ14) 46 50 55: 138 type=196 (LJ14) 46 58 55: 139 type=203 (LJ14) 47 53 55: 140 type=203 (LJ14) 47 55 55: 141 type=204 (LJ14) 47 56 55: 142 type=205 (LJ14) 47 58 55: 143 type=203 (LJ14) 48 51 55: 144 type=204 (LJ14) 48 54 55: 145 type=203 (LJ14) 48 57 55: 146 type=203 (LJ14) 49 50 55: 147 type=206 (LJ14) 49 53 55: 148 type=203 (LJ14) 49 56 55: 149 type=204 (LJ14) 50 52 55: 150 type=203 (LJ14) 50 57 55: 151 type=206 (LJ14) 51 55 55: 152 type=203 (LJ14) 51 56 55: 153 type=203 (LJ14) 52 55 55: 154 type=203 (LJ14) 53 54 55: 155 type=206 (LJ14) 53 57 55: 156 type=206 (LJ14) 55 57 55: 157 type=196 (LJ14) 58 63 55: 158 type=196 (LJ14) 58 64 55: 159 type=198 (LJ14) 58 65 55: 160 type=190 (LJ14) 59 61 55: 161 type=195 (LJ14) 59 62 55: 162 type=188 (LJ14) 60 66 55: 163 type=189 (LJ14) 60 67 55: 164 type=190 (LJ14) 61 63 55: 165 type=190 (LJ14) 61 64 55: 166 type=190 (LJ14) 61 65 55: 167 type=190 (LJ14) 62 68 55: 168 type=192 (LJ14) 62 69 55: 169 type=194 (LJ14) 63 66 55: 170 type=186 (LJ14) 63 67 55: 171 type=194 (LJ14) 64 66 55: 172 type=186 (LJ14) 64 67 55: 173 type=196 (LJ14) 65 70 55: 174 type=197 (LJ14) 65 71 55: 175 type=198 (LJ14) 65 89 55: 176 type=190 (LJ14) 66 68 55: 177 type=195 (LJ14) 66 69 55: 178 type=186 (LJ14) 67 72 55: 179 type=186 (LJ14) 67 73 55: 180 type=187 (LJ14) 67 74 55: 181 type=188 (LJ14) 67 90 55: 182 type=189 (LJ14) 67 91 55: 183 type=190 (LJ14) 68 70 55: 184 type=190 (LJ14) 68 71 55: 185 type=190 (LJ14) 68 89 55: 186 type=191 (LJ14) 69 75 55: 187 type=191 (LJ14) 69 76 55: 188 type=192 (LJ14) 69 77 55: 189 type=190 (LJ14) 69 92 55: 190 type=192 (LJ14) 69 93 55: 191 type=193 (LJ14) 70 72 55: 192 type=193 (LJ14) 70 73 55: 193 type=191 (LJ14) 70 74 55: 194 type=194 (LJ14) 70 90 55: 195 type=186 (LJ14) 70 91 55: 196 type=191 (LJ14) 71 78 55: 197 type=191 (LJ14) 71 79 55: 198 type=187 (LJ14) 71 80 55: 199 type=195 (LJ14) 71 90 55: 200 type=187 (LJ14) 71 91 55: 201 type=193 (LJ14) 72 75 55: 202 type=193 (LJ14) 72 76 55: 203 type=191 (LJ14) 72 77 55: 204 type=196 (LJ14) 72 89 55: 205 type=193 (LJ14) 73 75 55: 206 type=193 (LJ14) 73 76 55: 207 type=191 (LJ14) 73 77 55: 208 type=196 (LJ14) 73 89 55: 209 type=190 (LJ14) 74 81 55: 210 type=207 (LJ14) 74 82 55: 211 type=197 (LJ14) 74 89 55: 212 type=193 (LJ14) 75 78 55: 213 type=193 (LJ14) 75 79 55: 214 type=186 (LJ14) 75 80 55: 215 type=193 (LJ14) 76 78 55: 216 type=193 (LJ14) 76 79 55: 217 type=186 (LJ14) 76 80 55: 218 type=187 (LJ14) 77 83 55: 219 type=187 (LJ14) 77 86 55: 220 type=190 (LJ14) 78 81 55: 221 type=208 (LJ14) 78 82 55: 222 type=190 (LJ14) 79 81 55: 223 type=208 (LJ14) 79 82 55: 224 type=190 (LJ14) 80 84 55: 225 type=190 (LJ14) 80 85 55: 226 type=190 (LJ14) 80 87 55: 227 type=190 (LJ14) 80 88 55: 228 type=190 (LJ14) 81 83 55: 229 type=190 (LJ14) 81 86 55: 230 type=190 (LJ14) 83 87 55: 231 type=190 (LJ14) 83 88 55: 232 type=190 (LJ14) 84 86 55: 233 type=190 (LJ14) 85 86 55: 234 type=196 (LJ14) 89 94 55: 235 type=197 (LJ14) 89 95 55: 236 type=198 (LJ14) 89 100 55: 237 type=190 (LJ14) 90 92 55: 238 type=195 (LJ14) 90 93 55: 239 type=186 (LJ14) 91 96 55: 240 type=186 (LJ14) 91 97 55: 241 type=209 (LJ14) 91 98 55: 242 type=188 (LJ14) 91 101 55: 243 type=189 (LJ14) 91 102 55: 244 type=190 (LJ14) 92 94 55: 245 type=190 (LJ14) 92 95 55: 246 type=190 (LJ14) 92 100 55: 247 type=190 (LJ14) 93 99 55: 248 type=190 (LJ14) 93 103 55: 249 type=192 (LJ14) 93 104 55: 250 type=193 (LJ14) 94 96 55: 251 type=193 (LJ14) 94 97 55: 252 type=210 (LJ14) 94 98 55: 253 type=194 (LJ14) 94 101 55: 254 type=186 (LJ14) 94 102 55: 255 type=195 (LJ14) 95 101 55: 256 type=187 (LJ14) 95 102 55: 257 type=190 (LJ14) 96 99 55: 258 type=196 (LJ14) 96 100 55: 259 type=190 (LJ14) 97 99 55: 260 type=196 (LJ14) 97 100 55: 261 type=211 (LJ14) 98 100 55: 262 type=196 (LJ14) 100 105 55: 263 type=197 (LJ14) 100 106 55: 264 type=198 (LJ14) 100 115 55: 265 type=190 (LJ14) 101 103 55: 266 type=195 (LJ14) 101 104 55: 267 type=186 (LJ14) 102 107 55: 268 type=186 (LJ14) 102 108 55: 269 type=187 (LJ14) 102 109 55: 270 type=188 (LJ14) 102 116 55: 271 type=189 (LJ14) 102 117 55: 272 type=190 (LJ14) 103 105 55: 273 type=190 (LJ14) 103 106 55: 274 type=190 (LJ14) 103 115 55: 275 type=191 (LJ14) 104 110 55: 276 type=191 (LJ14) 104 111 55: 277 type=197 (LJ14) 104 112 55: 278 type=190 (LJ14) 104 118 55: 279 type=192 (LJ14) 104 119 55: 280 type=193 (LJ14) 105 107 55: 281 type=193 (LJ14) 105 108 55: 282 type=191 (LJ14) 105 109 55: 283 type=194 (LJ14) 105 116 55: 284 type=186 (LJ14) 105 117 55: 285 type=195 (LJ14) 106 113 55: 286 type=195 (LJ14) 106 114 55: 287 type=195 (LJ14) 106 116 55: 288 type=187 (LJ14) 106 117 55: 289 type=193 (LJ14) 107 110 55: 290 type=193 (LJ14) 107 111 55: 291 type=196 (LJ14) 107 112 55: 292 type=196 (LJ14) 107 115 55: 293 type=193 (LJ14) 108 110 55: 294 type=193 (LJ14) 108 111 55: 295 type=196 (LJ14) 108 112 55: 296 type=196 (LJ14) 108 115 55: 297 type=197 (LJ14) 109 115 55: 298 type=194 (LJ14) 110 113 55: 299 type=194 (LJ14) 110 114 55: 300 type=194 (LJ14) 111 113 55: 301 type=194 (LJ14) 111 114 55: 302 type=196 (LJ14) 115 120 55: 303 type=197 (LJ14) 115 121 55: 304 type=198 (LJ14) 115 134 55: 305 type=190 (LJ14) 116 118 55: 306 type=195 (LJ14) 116 119 55: 307 type=186 (LJ14) 117 122 55: 308 type=186 (LJ14) 117 123 55: 309 type=187 (LJ14) 117 124 55: 310 type=188 (LJ14) 117 135 55: 311 type=189 (LJ14) 117 136 55: 312 type=190 (LJ14) 118 120 55: 313 type=190 (LJ14) 118 121 55: 314 type=190 (LJ14) 118 134 55: 315 type=191 (LJ14) 119 125 55: 316 type=192 (LJ14) 119 126 55: 317 type=192 (LJ14) 119 130 55: 318 type=190 (LJ14) 119 137 55: 319 type=192 (LJ14) 119 138 55: 320 type=193 (LJ14) 120 122 55: 321 type=193 (LJ14) 120 123 55: 322 type=191 (LJ14) 120 124 55: 323 type=194 (LJ14) 120 135 55: 324 type=186 (LJ14) 120 136 55: 325 type=191 (LJ14) 121 127 55: 326 type=191 (LJ14) 121 128 55: 327 type=191 (LJ14) 121 129 55: 328 type=191 (LJ14) 121 131 55: 329 type=191 (LJ14) 121 132 55: 330 type=191 (LJ14) 121 133 55: 331 type=195 (LJ14) 121 135 55: 332 type=187 (LJ14) 121 136 55: 333 type=193 (LJ14) 122 125 55: 334 type=191 (LJ14) 122 126 55: 335 type=191 (LJ14) 122 130 55: 336 type=196 (LJ14) 122 134 55: 337 type=193 (LJ14) 123 125 55: 338 type=191 (LJ14) 123 126 55: 339 type=191 (LJ14) 123 130 55: 340 type=196 (LJ14) 123 134 55: 341 type=197 (LJ14) 124 134 55: 342 type=193 (LJ14) 125 127 55: 343 type=193 (LJ14) 125 128 55: 344 type=193 (LJ14) 125 129 55: 345 type=193 (LJ14) 125 131 55: 346 type=193 (LJ14) 125 132 55: 347 type=193 (LJ14) 125 133 55: 348 type=191 (LJ14) 126 131 55: 349 type=191 (LJ14) 126 132 55: 350 type=191 (LJ14) 126 133 55: 351 type=191 (LJ14) 127 130 55: 352 type=191 (LJ14) 128 130 55: 353 type=191 (LJ14) 129 130 55: 354 type=196 (LJ14) 134 139 55: 355 type=197 (LJ14) 134 140 55: 356 type=198 (LJ14) 134 144 55: 357 type=190 (LJ14) 135 137 55: 358 type=195 (LJ14) 135 138 55: 359 type=186 (LJ14) 136 141 55: 360 type=186 (LJ14) 136 142 55: 361 type=186 (LJ14) 136 143 55: 362 type=188 (LJ14) 136 145 55: 363 type=189 (LJ14) 136 146 55: 364 type=190 (LJ14) 137 139 55: 365 type=190 (LJ14) 137 140 55: 366 type=190 (LJ14) 137 144 55: 367 type=190 (LJ14) 138 147 55: 368 type=192 (LJ14) 138 148 55: 369 type=193 (LJ14) 139 141 55: 370 type=193 (LJ14) 139 142 55: 371 type=193 (LJ14) 139 143 55: 372 type=194 (LJ14) 139 145 55: 373 type=186 (LJ14) 139 146 55: 374 type=195 (LJ14) 140 145 55: 375 type=187 (LJ14) 140 146 55: 376 type=196 (LJ14) 141 144 55: 377 type=196 (LJ14) 142 144 55: 378 type=196 (LJ14) 143 144 55: 379 type=196 (LJ14) 144 149 55: 380 type=197 (LJ14) 144 150 55: 381 type=198 (LJ14) 144 154 55: 382 type=190 (LJ14) 145 147 55: 383 type=195 (LJ14) 145 148 55: 384 type=186 (LJ14) 146 151 55: 385 type=186 (LJ14) 146 152 55: 386 type=186 (LJ14) 146 153 55: 387 type=188 (LJ14) 146 155 55: 388 type=190 (LJ14) 147 149 55: 389 type=190 (LJ14) 147 150 55: 390 type=190 (LJ14) 147 154 55: 391 type=193 (LJ14) 149 151 55: 392 type=193 (LJ14) 149 152 55: 393 type=193 (LJ14) 149 153 55: 394 type=194 (LJ14) 149 155 55: 395 type=195 (LJ14) 150 155 55: 396 type=196 (LJ14) 151 154 55: 397 type=196 (LJ14) 152 154 55: 398 type=196 (LJ14) 153 154 55: Coulomb-14: 55: nr: 0 55: LJC-14 q: 55: nr: 0 55: LJC Pairs NB: 55: nr: 0 55: LJ (SR): 55: nr: 0 55: Buck.ham (SR): 55: nr: 0 55: LJ (unused): 55: nr: 0 55: B.ham (unused): 55: nr: 0 55: Disper. corr.: 55: nr: 0 55: Coulomb (SR): 55: nr: 0 55: Coul (unused): 55: nr: 0 55: RF excl.: 55: nr: 0 55: Coul. recip.: 55: nr: 0 55: LJ recip.: 55: nr: 0 55: DPD: 55: nr: 0 55: Polarization: 55: nr: 0 55: Water Pol.: 55: nr: 0 55: Thole Pol.: 55: nr: 0 55: Anharm. Pol.: 55: nr: 0 55: Position Rest.: 55: nr: 0 55: Flat-b. P-R.: 55: nr: 0 55: Dis. Rest.: 55: nr: 0 55: D.R.Viol. (nm): 55: nr: 0 55: Orient. Rest.: 55: nr: 0 55: Ori. R. RMSD: 55: nr: 0 55: Angle Rest.: 55: nr: 0 55: Angle Rest. Z: 55: nr: 0 55: Dih. Rest.: 55: nr: 0 55: Dih. Rest. Viol.: 55: nr: 0 55: Constraint: 55: nr: 0 55: Constr. No Conn.: 55: nr: 0 55: Settle: 55: nr: 0 55: Virtual site 1: 55: nr: 0 55: Virtual site 2: 55: nr: 0 55: Virtual site 2fd: 55: nr: 0 55: Virtual site 3: 55: nr: 0 55: Virtual site 3fd: 55: nr: 0 55: Virtual site 3fad: 55: nr: 0 55: Virtual site 3out: 55: nr: 0 55: Virtual site 4fd: 55: nr: 0 55: Virtual site 4fdn: 55: nr: 0 55: Virtual site N: 55: nr: 0 55: COM Pull En.: 55: nr: 0 55: Dens. fitting: 55: nr: 0 55: Quantum En.: 55: nr: 0 55: Potential: 55: nr: 0 55: Kinetic En.: 55: nr: 0 55: Total Energy: 55: nr: 0 55: Conserved En.: 55: nr: 0 55: Temperature: 55: nr: 0 55: Vir. Temp. (not used): 55: nr: 0 55: Pres. DC: 55: nr: 0 55: Pressure: 55: nr: 0 55: dH/dl constr.: 55: nr: 0 55: dVremain/dl: 55: nr: 0 55: dEkin/dl: 55: nr: 0 55: dVcoul/dl: 55: nr: 0 55: dVvdw/dl: 55: nr: 0 55: dVbonded/dl: 55: nr: 0 55: dVrestraint/dl: 55: nr: 0 55: dVtemperature/dl: 55: nr: 0 55: grp[T-Coupling ] nr=1, name=[ rest] 55: grp[Energy Mon. ] nr=1, name=[ rest] 55: grp[Acc. not used] nr=1, name=[ rest] 55: grp[Freeze ] nr=1, name=[ rest] 55: grp[User1 ] nr=1, name=[ rest] 55: grp[User2 ] nr=1, name=[ rest] 55: grp[VCM ] nr=1, name=[ rest] 55: grp[Compressed X] nr=1, name=[ rest] 55: grp[Or. Res. Fit] nr=1, name=[ rest] 55: grp[QMMM ] nr=1, name=[ rest] 55: grpname (11): 55: grpname[0]={name="System"} 55: grpname[1]={name="Protein"} 55: grpname[2]={name="Protein-H"} 55: grpname[3]={name="C-alpha"} 55: grpname[4]={name="Backbone"} 55: grpname[5]={name="MainChain"} 55: grpname[6]={name="MainChain+Cb"} 55: grpname[7]={name="MainChain+H"} 55: grpname[8]={name="SideChain"} 55: grpname[9]={name="SideChain-H"} 55: grpname[10]={name="rest"} 55: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 55: allocated 0 0 0 0 0 0 0 0 0 0 55: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 55: box (3x3): 55: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 55: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 55: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 55: box_rel (3x3): 55: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: boxv (3x3): 55: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: pres_prev (3x3): 55: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: svir_prev (3x3): 55: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: fvir_prev (3x3): 55: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: nosehoover_xi: not available 55: x (156x3): 55: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 55: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 55: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 55: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 55: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 55: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 55: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 55: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 55: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 55: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 55: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 55: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 55: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 55: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 55: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 55: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 55: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 55: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 55: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 55: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 55: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 55: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 55: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 55: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 55: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 55: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 55: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 55: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 55: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 55: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 55: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 55: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 55: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 55: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 55: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 55: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 55: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 55: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 55: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 55: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 55: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 55: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 55: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 55: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 55: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 55: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 55: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 55: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 55: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 55: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 55: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 55: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 55: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 55: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 55: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 55: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 55: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 55: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 55: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 55: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 55: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 55: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 55: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 55: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 55: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 55: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 55: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 55: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 55: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 55: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 55: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 55: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 55: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 55: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 55: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 55: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 55: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 55: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 55: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 55: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 55: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 55: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 55: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 55: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 55: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 55: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 55: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 55: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 55: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 55: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 55: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 55: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 55: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 55: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 55: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 55: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 55: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 55: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 55: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 55: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 55: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 55: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 55: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 55: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 55: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 55: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 55: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 55: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 55: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 55: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 55: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 55: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 55: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 55: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 55: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 55: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 55: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 55: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 55: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 55: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 55: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 55: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 55: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 55: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 55: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 55: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 55: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 55: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 55: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 55: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 55: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 55: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 55: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 55: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 55: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 55: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 55: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 55: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 55: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 55: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 55: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 55: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 55: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 55: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 55: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 55: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 55: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 55: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 55: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 55: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 55: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 55: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 55: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 55: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 55: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 55: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 55: v (156x3): 55: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 55: Group statistics 55: T-Coupling : 156 (total 156 atoms) 55: Energy Mon. : 156 (total 156 atoms) 55: Acc. not used: 156 (total 156 atoms) 55: Freeze : 156 (total 156 atoms) 55: User1 : 156 (total 156 atoms) 55: User2 : 156 (total 156 atoms) 55: VCM : 156 (total 156 atoms) 55: Compressed X: 156 (total 156 atoms) 55: Or. Res. Fit: 156 (total 156 atoms) 55: QMMM : 156 (total 156 atoms) 55: [ OK ] DumpTest.WorksWithTpr (67 ms) 55: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: [ OK ] DumpTest.WorksWithTprAndMdpWriting (1 ms) 55: [----------] 2 tests from DumpTest (68 ms total) 55: 55: [----------] 3 tests from HelpwritingTest 55: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 55: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 55: [ RUN ] HelpwritingTest.DumpWritesHelp 55: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 55: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 55: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (28 ms) 55: [----------] 3 tests from HelpwritingTest (29 ms total) 55: 55: [----------] 4 tests from ReportMethodsTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Setting the LD random seed to -77663795 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 55: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 55: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 55: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 55: [ RUN ] ReportMethodsTest.WritesCorrectInformation 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: [ OK ] ReportMethodsTest.WritesCorrectInformation (9 ms) 55: [ RUN ] ReportMethodsTest.ToolEndToEndTest 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: section: Methods 55: subsection: Simulation system 55: A system of 1 molecules (156 atoms) was simulated. 55: 55: subsection: Simulation settings 55: A total of 0 ns were simulated with a time step of 1 fs. 55: Neighbor searching was performed every 10 steps. 55: The Cut-off algorithm was used for electrostatic interactions. 55: with a cut-off of 1 nm. 55: A single cut-off of 1.1 nm was used for Van der Waals interactions. 55: [ OK ] ReportMethodsTest.ToolEndToEndTest (1 ms) 55: [----------] 4 tests from ReportMethodsTest (10 ms total) 55: 55: [----------] 3 tests from ConvertTprTest 55: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Setting the LD random seed to -1368556809 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 0 55: Runtime for the run 0 ps 55: Run end step 0 55: Run end time 0 ps 55: 55: Extending remaining runtime by 100 ps 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 100000 55: Runtime for the run 100 ps 55: Run end step 100000 55: Run end time 100 ps 55: 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 100000 55: Runtime for the run 100 ps 55: Run end step 100000 55: Run end time 100 ps 55: 55: Extending remaining runtime by 100 ps 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 200000 55: Runtime for the run 200 ps 55: Run end step 200000 55: Run end time 200 ps 55: 55: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (1542 ms) 55: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Setting the LD random seed to -1678780641 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 0 55: Runtime for the run 0 ps 55: Run end step 0 55: Run end time 0 ps 55: 55: Extending remaining runtime to 100 ps 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 100000 55: Runtime for the run 100 ps 55: Run end step 100000 55: Run end time 100 ps 55: 55: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (1433 ms) 55: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 55: 55: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 55: For a correct single-point energy evaluation with nsteps = 0, use 55: continuation = yes to avoid constraining the input coordinates. 55: 55: Generating 1-4 interactions: fudge = 0.5 55: 55: NOTE 2 [file lysozyme.top, line 1465]: 55: System has non-zero total charge: 2.000000 55: Total charge should normally be an integer. See 55: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 55: for discussion on how close it should be to an integer. 55: 55: 55: 55: Number of degrees of freedom in T-Coupling group rest is 465.00 55: 55: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 55: NVE simulation with an initial temperature of zero: will use a Verlet 55: buffer of 10%. Check your energy drift! 55: 55: 55: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 55: You are using a plain Coulomb cut-off, which might produce artifacts. 55: You might want to consider using PME electrostatics. 55: 55: 55: 55: There were 4 notes 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Setting nsteps to 102 55: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 55: Setting the LD random seed to -34212613 55: 55: Generated 330891 of the 330891 non-bonded parameter combinations 55: 55: Generated 330891 of the 330891 1-4 parameter combinations 55: 55: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 55: Analysing residue names: 55: There are: 10 Protein residues 55: Analysing Protein... 55: 55: This run will generate roughly 0 Mb of data 55: Input file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 0 55: Runtime for the run 0 ps 55: Run end step 0 55: Run end time 0 ps 55: 55: 55: Output file: 55: Run start step 0 55: Run start time 0 ps 55: Step to be made during run 102 55: Runtime for the run 0.102 ps 55: Run end step 102 55: Run end time 0.102 ps 55: 55: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (694 ms) 55: [----------] 3 tests from ConvertTprTest (3671 ms total) 55: 55: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: trr version: GMX_trn_file (single precision) 55: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (1 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (1 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (4 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (1 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (8 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 55: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 55: Will write trr: Trajectory in portable xdr format 55: Group 0 ( System) has 6 elements 55: Group 1 (FirstWaterMolecule) has 3 elements 55: Group 2 (SecondWaterMolecule) has 3 elements 55: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 55: -> frame 1 time 1.000 55: Last written: frame 1 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: Select group for output 55: Selected 2: 'SecondWaterMolecule' 55: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 55: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (21 ms total) 55: 55: [----------] 30 tests from Works/TrjconvDumpTest 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (2 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (2 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (1 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (2 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 55: Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 55: Precision of /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 55: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 55: Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (4 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 0 ps 55: -> frame 0 time 0.000 55: Last written: frame 0 time 0.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 55: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 55: Will write trr: Trajectory in portable xdr format 55: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 55: 55: Dumping frame at t= 1 ps 55: -> frame 0 time 1.000 55: Last written: frame 0 time 1.000 55: 55: 55: Note that major changes are planned in future for trjconv, to improve usability and utility. 55: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 55: [----------] 30 tests from Works/TrjconvDumpTest (29 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 54 tests from 6 test suites ran. (5909 ms total) 55: [ PASSED ] 54 tests. 55/81 Test #55: ToolUnitTests .................................. Passed 7.39 sec test 56 Start 56: FileIOTests 56: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/FileIOTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/fileio/tests 56: Test timeout computed to be: 30 56: [==========] Running 42 tests from 10 test suites. 56: [----------] Global test environment set-up. 56: [----------] 4 tests from Checkpoint 56: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 56: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 56: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 56: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 56: [ RUN ] Checkpoint.KvtRoundTripInt64 56: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 56: [ RUN ] Checkpoint.KvtRoundTripReal 56: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 56: [----------] 4 tests from Checkpoint (0 ms total) 56: 56: [----------] 2 tests from FileMD5Test 56: [ RUN ] FileMD5Test.CanComputeMD5 56: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 56: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 56: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 56: [----------] 2 tests from FileMD5Test (1 ms total) 56: 56: [----------] 3 tests from MrcSerializer 56: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 56: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 56: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 56: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 56: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 56: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 56: [----------] 3 tests from MrcSerializer (0 ms total) 56: 56: [----------] 4 tests from MrcDensityMap 56: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 56: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 56: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 56: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 56: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 56: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 56: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 56: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (1 ms) 56: [----------] 4 tests from MrcDensityMap (2 ms total) 56: 56: [----------] 8 tests from MrcDensityMapHeaderTest 56: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 56: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 56: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 56: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 56: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 56: [ RUN ] MrcDensityMapHeaderTest.IsSane 56: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 56: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 56: 56: [----------] 10 tests from ReadTest 56: [ RUN ] ReadTest.get_eint_ReadsInteger 56: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 56: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side '0.8' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 56: [ RUN ] ReadTest.get_eint_WarnsAboutString 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side 'hello' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 56: [ RUN ] ReadTest.get_eint64_ReadsInteger 56: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 56: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side '0.8' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 56: [ RUN ] ReadTest.get_eint64_WarnsAboutString 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side 'hello' for parameter 'test' in parameter file is not an 56: integer value 56: 56: 56: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 56: [ RUN ] ReadTest.get_ereal_ReadsInteger 56: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 56: [ RUN ] ReadTest.get_ereal_ReadsFloat 56: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 56: [ RUN ] ReadTest.get_ereal_WarnsAboutString 56: 56: ERROR 1 [file unknown, line 0]: 56: Right hand side 'hello' for parameter 'test' in parameter file is not a 56: real value 56: 56: 56: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 56: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 56: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 56: [----------] 10 tests from ReadTest (0 ms total) 56: 56: [----------] 1 test from FileIOXdrSerializerTest 56: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 56: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 56: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 56: 56: [----------] 2 tests from TngTest 56: [ RUN ] TngTest.CanOpenTngFile 56: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 56: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890 56: [ OK ] TngTest.CanOpenTngFile (0 ms) 56: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 56: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 56: [----------] 2 tests from TngTest (0 ms total) 56: 56: [----------] 4 tests from XvgioTest 56: [ RUN ] XvgioTest.readXvgIntWorks 56: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 56: [ RUN ] XvgioTest.readXvgRealWorks 56: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 56: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 56: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 56: [ RUN ] XvgioTest.readXvgDeprecatedWorks 56: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 56: [----------] 4 tests from XvgioTest (0 ms total) 56: 56: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 56: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 56: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 56: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (1 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 42 tests from 10 test suites ran. (7 ms total) 56: [ PASSED ] 42 tests. 56/81 Test #56: FileIOTests .................................... Passed 1.29 sec test 57 Start 57: SelectionUnitTests 57: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/SelectionUnitTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/gromacs/selection/tests 57: Test timeout computed to be: 30 57: [==========] Running 201 tests from 11 test suites. 57: [----------] Global test environment set-up. 57: [----------] 1 test from IndexGroupTest 57: [ RUN ] IndexGroupTest.RemovesDuplicates 57: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 57: [----------] 1 test from IndexGroupTest (0 ms total) 57: 57: [----------] 15 tests from IndexBlockTest 57: [ RUN ] IndexBlockTest.CreatesUnknownBlock 57: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 57: [ RUN ] IndexBlockTest.CreatesAtomBlock 57: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 57: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 57: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 57: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 57: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 57: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 57: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 57: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 57: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 57: [ RUN ] IndexBlockTest.CreatesSingleBlock 57: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 57: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 57: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 57: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 57: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 57: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 57: [----------] 15 tests from IndexBlockTest (1 ms total) 57: 57: [----------] 11 tests from IndexMapTest 57: [ RUN ] IndexMapTest.InitializesAtomBlock 57: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 57: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 57: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 57: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 57: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 57: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 57: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 57: [ RUN ] IndexMapTest.InitializesMoleculeBlock 57: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 57: [ RUN ] IndexMapTest.MapsSingleBlock 57: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 57: [ RUN ] IndexMapTest.MapsResidueBlocks 57: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 57: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 57: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 57: [ RUN ] IndexMapTest.HandlesMultipleRequests 57: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 57: [----------] 11 tests from IndexMapTest (5 ms total) 57: 57: [----------] 3 tests from IndexGroupsAndNamesTest 57: [ RUN ] IndexGroupsAndNamesTest.containsNames 57: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 57: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 57: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 57: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 57: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 57: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 57: 57: [----------] 15 tests from NeighborhoodSearchTest 57: [ RUN ] NeighborhoodSearchTest.SimpleSearch 57: [ OK ] NeighborhoodSearchTest.SimpleSearch (47 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 57: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (38 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchBox 57: [ OK ] NeighborhoodSearchTest.GridSearchBox (2 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 57: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (23 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 57: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (14 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 57: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (1 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 57: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (11 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 57: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (128 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 57: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 57: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 57: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 57: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 57: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 57: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 57: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (8 ms) 57: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 57: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 57: [----------] 15 tests from NeighborhoodSearchTest (287 ms total) 57: 57: [----------] 13 tests from PositionCalculationTest 57: [ RUN ] PositionCalculationTest.ComputesAtomPositions 57: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 57: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 57: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 57: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 57: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 57: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 57: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 57: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 57: [ RUN ] PositionCalculationTest.ComputesPositionMask 57: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 57: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 57: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 57: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 57: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 57: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 57: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 57: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 57: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 57: [----------] 13 tests from PositionCalculationTest (12 ms total) 57: 57: [----------] 33 tests from SelectionCollectionTest 57: [ RUN ] SelectionCollectionTest.HandlesNoSelections 57: [ OK ] SelectionCollectionTest.HandlesNoSelections (8 ms) 57: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 57: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 57: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 57: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 57: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 57: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 57: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 57: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 57: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 57: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 57: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (6 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 57: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 57: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 57: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 57: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 57: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 57: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 57: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (4 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 57: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 57: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 57: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 57: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 57: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 57: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (8 ms) 57: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 57: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 57: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 57: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 57: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 57: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 57: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 57: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 57: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 57: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 57: [----------] 33 tests from SelectionCollectionTest (43 ms total) 57: 57: [----------] 14 tests from SelectionCollectionInteractiveTest 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 57: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (8 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 57: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 57: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 57: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 57: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 57: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 57: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 57: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 57: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 57: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 57: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 57: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 57: [----------] 14 tests from SelectionCollectionInteractiveTest (16 ms total) 57: 57: [----------] 70 tests from SelectionCollectionDataTest 57: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 57: [ OK ] SelectionCollectionDataTest.HandlesAllNone (8 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 57: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesResnr 57: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 57: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 57: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 57: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 57: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (5 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 57: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesChain 57: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMass 57: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesCharge 57: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 57: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (4 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 57: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 57: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBeta 57: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesResname 57: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 57: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (9 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 57: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 57: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 57: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (5 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 57: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (12 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (6 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (6 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 57: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (2 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (10 ms) 57: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 57: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 57: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 57: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 57: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 57: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (10 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 57: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 57: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (9 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 57: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 57: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 57: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 57: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 57: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 57: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 57: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 57: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (8 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 57: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 57: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 57: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 57: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 57: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (5 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 57: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 57: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (9 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 57: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (5 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 57: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 57: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 57: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (5 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 57: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (1 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 57: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 57: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 57: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 57: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (8 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 57: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 57: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 57: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (6 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (2 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (2 ms) 57: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 57: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (2 ms) 57: [----------] 70 tests from SelectionCollectionDataTest (194 ms total) 57: 57: [----------] 17 tests from SelectionOptionTest 57: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 57: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 57: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 57: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 57: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 57: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 57: [ RUN ] SelectionOptionTest.ChecksEmptySelections 57: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 57: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 57: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (2 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooManySelections 57: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 57: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 57: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesAdjuster 57: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 57: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 57: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 57: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 57: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 57: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 57: [----------] 17 tests from SelectionOptionTest (7 ms total) 57: 57: [----------] 9 tests from SelectionFileOptionTest 57: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 57: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 57: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 57: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 57: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 57: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 57: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 57: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (4 ms) 57: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 57: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 57: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 57: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 57: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 57: [----------] 9 tests from SelectionFileOptionTest (7 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 201 tests from 11 test suites ran. (576 ms total) 57: [ PASSED ] 201 tests. 57/81 Test #57: SelectionUnitTests ............................. Passed 1.81 sec test 58 Start 58: MdrunOutputTests 58: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunOutputTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 58: Test timeout computed to be: 600 58: [==========] Running 12 tests from 5 test suites. 58: [----------] Global test environment set-up. 58: [----------] 1 test from MdrunTest 58: [ RUN ] MdrunTest.WritesHelp 58: [ OK ] MdrunTest.WritesHelp (149 ms) 58: [----------] 1 test from MdrunTest (149 ms total) 58: 58: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 58: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 58: Generating 1-4 interactions: fudge = 0.5 58: Number of degrees of freedom in T-Coupling group rest is 9.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 58: NVE simulation: will use the initial temperature of 2573.591 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 2 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI process 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc2' 58: 1 steps, 0.0 ps. 58: Setting the LD random seed to 1071363067 58: 58: Generated 3 of the 3 non-bonded parameter combinations 58: 58: Generated 3 of the 3 1-4 parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.005 0.003 195.0 58: (ns/day) (hour/ns) 58: Performance: 63.233 0.380 58: Reading frame 0 time 0.000 58: # Atoms 6 58: Reading frame 1 time 0.001 Last frame 1 time 0.001 58: 58: 58: Item #frames Timestep (ps) 58: Step 2 0.001 58: Time 2 0.001 58: Lambda 0 58: Coords 2 0.001 58: Velocities 0 58: Forces 0 58: Box 2 0.001 58: Checking file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 58: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (36 ms) 58: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 58: Generating 1-4 interactions: fudge = 0.5 58: Number of degrees of freedom in T-Coupling group rest is 9.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 58: NVE simulation: will use the initial temperature of 2573.591 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 2 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI process 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc2' 58: 1 steps, 0.0 ps. 58: Setting the LD random seed to 1002422013 58: 58: Generated 3 of the 3 non-bonded parameter combinations 58: 58: Generated 3 of the 3 1-4 parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.026 0.013 198.3 58: (ns/day) (hour/ns) 58: Performance: 13.336 1.800 58: Reading frame 0 time 0.000 58: # Atoms 6 58: Reading frame 1 time 0.001 Last frame 1 time 0.001 58: 58: 58: Item #frames Timestep (ps) 58: Step 2 0.001 58: Time 2 0.001 58: Lambda 0 58: Coords 2 0.001 58: Velocities 0 58: Forces 0 58: Box 2 0.001 58: Checking file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 58: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (24 ms) 58: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 58: Generating 1-4 interactions: fudge = 0.5 58: Number of degrees of freedom in T-Coupling group rest is 9.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 58: NVE simulation: will use the initial temperature of 2573.591 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 2 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI process 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc2' 58: 1 steps, 0.0 ps. 58: Setting the LD random seed to -178258061 58: 58: Generated 3 of the 3 non-bonded parameter combinations 58: 58: Generated 3 of the 3 1-4 parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.027 0.013 198.8 58: (ns/day) (hour/ns) 58: Performance: 12.850 1.868 58: Reading frame 0 time 0.000 58: # Atoms 3 58: Reading frame 1 time 0.001 Last frame 1 time 0.001 58: 58: 58: Item #frames Timestep (ps) 58: Step 2 0.001 58: Time 2 0.001 58: Lambda 0 58: Coords 2 0.001 58: Velocities 0 58: Forces 0 58: Box 2 0.001 58: Checking file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 58: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (29 ms) 58: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (90 ms total) 58: 58: [----------] 2 tests from Argon12/OutputFiles 58: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 58: that with the Verlet scheme, nstlist has no effect on the accuracy of 58: your simulation. 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 58: Setting nstcalcenergy (100) equal to nstenergy (4) 58: 58: Number of degrees of freedom in T-Coupling group System is 33.00 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 58: NVE simulation: will use the initial temperature of 68.810 K for 58: determining the Verlet buffer size 58: 58: 58: There were 3 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI process 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'Argon' 58: 16 steps, 0.0 ps. 58: Generated 1 of the 1 non-bonded parameter combinations 58: 58: Excluding 1 bonded neighbours molecule type 'Argon' 58: 58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.003 0.002 191.4 58: (ns/day) (hour/ns) 58: Performance: 826.482 0.029 58: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (30 ms) 58: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 58: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 58: that with the Verlet scheme, nstlist has no effect on the accuracy of 58: your simulation. 58: 58: 58: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 58: Setting nstcalcenergy (100) equal to nstenergy (4) 58: 58: Number of degrees of freedom in T-Coupling group System is 33.00 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 58: NVE simulation: will use the initial temperature of 68.810 K for 58: determining the Verlet buffer size 58: 58: 58: There were 3 notes 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Can not increase nstlist because an NVE ensemble is used 58: Using 1 MPI process 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'Argon' 58: 16 steps, 0.0 ps. 58: Generated 1 of the 1 non-bonded parameter combinations 58: 58: Excluding 1 bonded neighbours molecule type 'Argon' 58: 58: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.005 0.002 197.2 58: (ns/day) (hour/ns) 58: Performance: 597.304 0.040 58: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (39 ms) 58: [----------] 2 tests from Argon12/OutputFiles (70 ms total) 58: 58: [----------] 3 tests from MdrunCanWrite/Trajectories 58: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI process 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 6 steps, 0.0 ps. 58: Setting the LD random seed to -436477953 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.070 0.035 199.4 58: (ns/day) (hour/ns) 58: Performance: 17.196 1.396 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (56 ms) 58: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI process 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 6 steps, 0.0 ps. 58: Setting the LD random seed to -86784260 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.031 0.016 198.8 58: (ns/day) (hour/ns) 58: Performance: 38.884 0.617 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (39 ms) 58: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI process 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 6 steps, 0.0 ps. 58: Setting the LD random seed to 1860431645 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.067 0.033 199.3 58: (ns/day) (hour/ns) 58: Performance: 18.106 1.326 58: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (62 ms) 58: [----------] 3 tests from MdrunCanWrite/Trajectories (159 ms total) 58: 58: [----------] 3 tests from MdrunCanWrite/NptTrajectories 58: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI process 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 2 steps, 0.0 ps. 58: Setting the LD random seed to -1228030497 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.003 0.002 189.6 58: (ns/day) (hour/ns) 58: Performance: 154.646 0.155 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (19 ms) 58: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 58: 58: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 58: The Berendsen barostat does not generate any strictly correct ensemble, 58: and should not be used for new production simulations (in our opinion). 58: For isotropic scaling we would recommend the C-rescale barostat that also 58: ensures fast relaxation without oscillations, and for anisotropic scaling 58: you likely want to use the Parrinello-Rahman barostat. 58: 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: 58: There was 1 warning 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI process 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 2 steps, 0.0 ps. 58: Setting the LD random seed to -173539329 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.020 0.010 198.0 58: (ns/day) (hour/ns) 58: Performance: 25.748 0.932 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (26 ms) 58: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 58: Number of degrees of freedom in T-Coupling group System is 12.00 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There was 1 note 58: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 58: log). 58: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 58: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 58: 58: Using 1 MPI process 58: Using 2 OpenMP threads 58: 58: 58: NOTE: The number of threads is not equal to the number of (logical) cpus 58: and the -pin option is set to auto: will not pin threads to cpus. 58: This can lead to significant performance degradation. 58: Consider using -pin on (and -pinoffset in case you run multiple jobs). 58: starting mdrun 'spc-and-methanol' 58: 2 steps, 0.0 ps. 58: Setting the LD random seed to -388211214 58: 58: Generated 8 of the 10 non-bonded parameter combinations 58: 58: Excluding 2 bonded neighbours molecule type 'Methanol' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 58: 58: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: 58: Writing final coordinates. 58: 58: Core t (s) Wall t (s) (%) 58: Time: 0.003 0.002 189.0 58: (ns/day) (hour/ns) 58: Performance: 153.403 0.156 58: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (22 ms) 58: [----------] 3 tests from MdrunCanWrite/NptTrajectories (68 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 12 tests from 5 test suites ran. (1180 ms total) 58: [ PASSED ] 12 tests. 58/81 Test #58: MdrunOutputTests ............................... Passed 2.29 sec test 59 Start 59: MdrunModulesTests 59: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunModulesTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 59: Test timeout computed to be: 600 59: [==========] Running 15 tests from 3 test suites. 59: [----------] Global test environment set-up. 59: [----------] 9 tests from DensityFittingTest 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -3.8565256e+03 59: Maximum force = 4.5099883e+03 on atom 3 59: Norm of force = 1.6816850e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1803882521 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (57 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -9.8207734e+03 59: Maximum force = 7.3954834e+03 on atom 2 59: Norm of force = 2.7825089e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2079023103 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (99 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (0 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Overriding nsteps with value passed on the command line: 4 steps 59: 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 4 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 5 steps. 59: Potential Energy = -1.0954993e+04 59: Maximum force = 7.4724790e+03 on atom 2 59: Norm of force = 2.7758003e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -251988875 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (56 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (0 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -3.8565256e+03 59: Maximum force = 4.5099883e+03 on atom 3 59: Norm of force = 1.6816850e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 798949241 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (55 ms) 59: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = -2.7138664e+04 59: Maximum force = 6.7827656e+03 on atom 2 59: Norm of force = 1.9608866e+03 59: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -542136593 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (58 ms) 59: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 59: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (0 ms) 59: [ RUN ] DensityFittingTest.CheckpointWorks 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 59: Setting nstcalcenergy (100) equal to nstenergy (2) 59: 59: Number of degrees of freedom in T-Coupling group rest is 33.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 59: NVE simulation: will use the initial temperature of 68.810 K for 59: determining the Verlet buffer size 59: 59: 59: There were 2 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting mdrun 'Argon' 59: 2 steps, 0.0 ps. 59: Setting the LD random seed to -9131267 59: 59: Generated 1 of the 1 non-bonded parameter combinations 59: 59: Excluding 1 bonded neighbours molecule type 'Argon' 59: 59: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 59: 59: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 59: 59: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 59: 59: Note that mdrun will redetermine rlist based on the actual pair-list setup 59: 59: This run will generate roughly 0 Mb of data 59: 59: Writing final coordinates. 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.005 0.003 194.4 59: (ns/day) (hour/ns) 59: Performance: 96.192 0.250 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 59: Can not increase nstlist because an NVE ensemble is used 59: 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting mdrun 'Argon' 59: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 59: 59: Writing final coordinates. 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.002 0.001 189.4 59: (ns/day) (hour/ns) 59: Performance: 342.069 0.070 59: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (60 ms) 59: [----------] 9 tests from DensityFittingTest (388 ms total) 59: 59: [----------] 4 tests from MimicTest 59: [ RUN ] MimicTest.OneQuantumMol 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 21.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 59: NVE simulation with an initial temperature of zero: will use a Verlet 59: buffer of 10%. Check your energy drift! 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 59: 59: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: NOTE: 19 % of the run time was spent in pair search, 59: you might want to increase nstlist (this has no effect on accuracy) 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.001 0.000 187.8 59: (ns/day) (hour/ns) 59: Performance: 238.413 0.101 59: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -8537352 59: 59: Generated 10 of the 10 non-bonded parameter combinations 59: 59: Generated 10 of the 10 1-4 parameter combinations 59: 59: Excluding 2 bonded neighbours molecule type 'SOL' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.OneQuantumMol (25 ms) 59: [ RUN ] MimicTest.AllQuantumMol 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 21.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 59: NVE simulation with an initial temperature of zero: will use a Verlet 59: buffer of 10%. Check your energy drift! 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 59: 59: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: NOTE: 18 % of the run time was spent in pair search, 59: you might want to increase nstlist (this has no effect on accuracy) 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.001 0.000 187.5 59: (ns/day) (hour/ns) 59: Performance: 219.762 0.109 59: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1225674757 59: 59: Generated 10 of the 10 non-bonded parameter combinations 59: 59: Generated 10 of the 10 1-4 parameter combinations 59: 59: Excluding 2 bonded neighbours molecule type 'SOL' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.AllQuantumMol (39 ms) 59: [ RUN ] MimicTest.TwoQuantumMol 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 21.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 59: NVE simulation with an initial temperature of zero: will use a Verlet 59: buffer of 10%. Check your energy drift! 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 59: 59: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: NOTE: 21 % of the run time was spent in pair search, 59: you might want to increase nstlist (this has no effect on accuracy) 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.001 0.000 187.4 59: (ns/day) (hour/ns) 59: Performance: 244.526 0.098 59: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2145643775 59: 59: Generated 10 of the 10 non-bonded parameter combinations 59: 59: Generated 10 of the 10 1-4 parameter combinations 59: 59: Excluding 2 bonded neighbours molecule type 'SOL' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.TwoQuantumMol (19 ms) 59: [ RUN ] MimicTest.BondCuts 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 59: For a correct single-point energy evaluation with nsteps = 0, use 59: continuation = yes to avoid constraining the input coordinates. 59: 59: Generating 1-4 interactions: fudge = 0.5 59: Number of degrees of freedom in T-Coupling group rest is 66.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 59: NVE simulation: will use the initial temperature of 300.368 K for 59: determining the Verlet buffer size 59: 59: 59: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 3 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Can not increase nstlist because an NVE ensemble is used 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/ala.gro' 59: 59: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 59: Reading frame 0 time 0.000 Last frame 0 time 0.000 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.025 0.012 199.4 59: (ns/day) (hour/ns) 59: Performance: 6.953 3.452 59: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1686438135 59: 59: Generated 2211 of the 2211 non-bonded parameter combinations 59: 59: Generated 2211 of the 2211 1-4 parameter combinations 59: 59: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 59: 59: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 59: 59: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 59: 59: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 59: 59: Note that mdrun will redetermine rlist based on the actual pair-list setup 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] MimicTest.BondCuts (83 ms) 59: [----------] 4 tests from MimicTest (169 ms total) 59: 59: [----------] 2 tests from WithIntegrator/ImdTest 59: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 59: Generating 1-4 interactions: fudge = 1 59: 59: NOTE 1 [file glycine_vacuo.top, line 12]: 59: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 59: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 59: the time step of 2.0e-03 ps. 59: Maybe you forgot to change the constraints mdp option. 59: 59: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 59: Number of degrees of freedom in T-Coupling group System is 27.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 2 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34 59: 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: IMD: Enabled. This simulation will accept incoming IMD connections. 59: IMD: Pulling from IMD remote is enabled (-imdpull). 59: IMD: Setting port for connection requests to 0. 59: IMD: Setting up incoming socket. 59: IMD: Listening for IMD connection on port 35351. 59: IMD: -imdwait not set, starting simulation. 59: starting mdrun 'Glycine' 59: 2 steps, 0.0 ps. 59: Setting the LD random seed to -58818586 59: 59: Generated 20503 of the 20503 non-bonded parameter combinations 59: 59: Generated 17396 of the 20503 1-4 parameter combinations 59: 59: Excluding 3 bonded neighbours molecule type 'Glycine' 59: 59: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 59: 59: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 59: 59: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm 59: 59: Note that mdrun will redetermine rlist based on the actual pair-list setup 59: 59: This run will generate roughly 0 Mb of data 59: 59: Writing final coordinates. 59: 59: Core t (s) Wall t (s) (%) 59: Time: 0.003 0.002 187.1 59: (ns/day) (hour/ns) 59: Performance: 286.473 0.084 59: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (315 ms) 59: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 59: 59: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 59: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 59: apply to steep. 59: 59: Generating 1-4 interactions: fudge = 1 59: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 59: Number of degrees of freedom in T-Coupling group System is 27.00 59: 59: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 59: You are using a plain Coulomb cut-off, which might produce artifacts. 59: You might want to consider using PME electrostatics. 59: 59: 59: 59: There were 2 notes 59: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 59: log). 59: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 59: Using 1 MPI process 59: Using 2 OpenMP threads 59: 59: 59: NOTE: The number of threads is not equal to the number of (logical) cpus 59: and the -pin option is set to auto: will not pin threads to cpus. 59: This can lead to significant performance degradation. 59: Consider using -pin on (and -pinoffset in case you run multiple jobs). 59: 59: IMD: Enabled. This simulation will accept incoming IMD connections. 59: IMD: Pulling from IMD remote is enabled (-imdpull). 59: IMD: Setting port for connection requests to 0. 59: IMD: Setting up incoming socket. 59: IMD: Listening for IMD connection on port 47567. 59: IMD: -imdwait not set, starting simulation. 59: 59: Steepest Descents: 59: Tolerance (Fmax) = 1.00000e+01 59: Number of steps = 2 59: 59: Energy minimization reached the maximum number of steps before the forces 59: reached the requested precision Fmax < 10. 59: 59: writing lowest energy coordinates. 59: 59: Steepest Descents did not converge to Fmax < 10 in 3 steps. 59: Potential Energy = 1.1977064e+03 59: Maximum force = 1.7794877e+04 on atom 9 59: Norm of force = 7.8732901e+03 59: Setting the LD random seed to -1342517380 59: 59: Generated 20503 of the 20503 non-bonded parameter combinations 59: 59: Generated 17396 of the 20503 1-4 parameter combinations 59: 59: Excluding 3 bonded neighbours molecule type 'Glycine' 59: 59: This run will generate roughly 0 Mb of data 59: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (326 ms) 59: [----------] 2 tests from WithIntegrator/ImdTest (641 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 15 tests from 3 test suites ran. (1669 ms total) 59: [ PASSED ] 15 tests. 59/81 Test #59: MdrunModulesTests .............................. Passed 2.86 sec test 60 Start 60: MdrunIOTests 60: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunIOTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 60: Test timeout computed to be: 600 60: [==========] Running 66 tests from 13 test suites. 60: [----------] Global test environment set-up. 60: [----------] 5 tests from GromppTest 60: [ RUN ] GromppTest.EmptyMdpFileWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Setting the LD random seed to -874520645 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.EmptyMdpFileWorks (9 ms) 60: [ RUN ] GromppTest.SimulatedAnnealingWorks 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Simulated annealing for group rest: Periodic, 4 timepoints 60: Time (ps) Temperature (K) 60: 0.0 298.0 60: 2.0 320.0 60: 4.0 320.0 60: 6.0 298.0 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Setting the LD random seed to -1348167170 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.SimulatedAnnealingWorks (12 ms) 60: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Simulated annealing for group Methanol: Single, 3 timepoints 60: Time (ps) Temperature (K) 60: 0.0 298.0 60: 3.0 280.0 60: 6.0- 270.0 60: Simulated annealing for group SOL: Periodic, 4 timepoints 60: Time (ps) Temperature (K) 60: 0.0 298.0 60: 2.0 320.0 60: 4.0 320.0 60: 6.0 298.0 60: Number of degrees of freedom in T-Coupling group Methanol is 7.20 60: Number of degrees of freedom in T-Coupling group SOL is 4.80 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Setting the LD random seed to -1732874449 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (29 ms) 60: [ RUN ] GromppTest.ValidTransformationCoord 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Pull group 1 'SOL' has 3 atoms 60: Pull group 2 'Methanol' has 3 atoms 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 5 60: 2 3 2 0.613 nm 0.000 nm 60: 1 3 5 60: 2 3 2 0.613 nm 0.000 nm 60: 60: There were 3 notes 60: Setting the LD random seed to -1767409154 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] GromppTest.ValidTransformationCoord (36 ms) 60: [ RUN ] GromppTest.InvalidTransformationCoord 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Pull group 1 'SOL' has 3 atoms 60: Pull group 2 'Methanol' has 3 atoms 60: Number of degrees of freedom in T-Coupling group rest is 12.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 60: NVE simulation: will use the initial temperature of 1046.791 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 5 60: 2 3 2 0.613 nm 0.000 nm 60: 1 3 5 60: 2 3 2 Setting the LD random seed to -557197 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: [ OK ] GromppTest.InvalidTransformationCoord (19 ms) 60: [----------] 5 tests from GromppTest (108 ms total) 60: 60: [----------] 6 tests from MdrunTerminationTest 60: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to 1573780427 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: NOTE: 17 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.560 0.280 199.9 60: (ns/day) (hour/ns) 60: Performance: 0.925 25.937 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: NOTE: 13 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.504 0.252 199.9 60: (ns/day) (hour/ns) 60: Performance: 1.028 23.343 60: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (704 ms) 60: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 1, rlist from 1.024 to 1 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 100 steps, 0.1 ps. 60: 60: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 60: Setting the LD random seed to 2129067967 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: NOTE: 28 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.824 0.412 199.9 60: (ns/day) (hour/ns) 60: Performance: 0.419 57.246 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 102 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100 60: Runtime for the run 0.1 ps 60: Run end step 100 60: Run end time 0.1 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 102 60: Runtime for the run 0.102 ps 60: Run end step 102 60: Run end time 0.102 ps 60: 60: 60: Writing final coordinates. 60: 60: NOTE: 43 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.240 0.120 199.8 60: (ns/day) (hour/ns) 60: Performance: 73.396 0.327 60: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (715 ms) 60: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -553701449 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 187.8 60: (ns/day) (hour/ns) 60: Performance: 248.779 0.096 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 193.6 60: (ns/day) (hour/ns) 60: Performance: 214.558 0.112 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 6 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 6 60: Runtime for the run 0.006 ps 60: Run end step 6 60: Run end time 0.006 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 194.0 60: (ns/day) (hour/ns) 60: Performance: 247.420 0.097 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 8 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 6 60: Runtime for the run 0.006 ps 60: Run end step 6 60: Run end time 0.006 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 8 60: Runtime for the run 0.008 ps 60: Run end step 8 60: Run end time 0.008 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 194.1 60: (ns/day) (hour/ns) 60: Performance: 239.727 0.100 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: NOTE: 23 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.000 0.000 168.8 60: (ns/day) (hour/ns) 60: Performance: 353.205 0.068 60: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (88 ms) 60: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -3808130 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 188.0 60: (ns/day) (hour/ns) 60: Performance: 259.838 0.092 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps. 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 188.3 60: (ns/day) (hour/ns) 60: Performance: 354.448 0.068 60: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (25 ms) 60: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -151540764 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 188.0 60: (ns/day) (hour/ns) 60: Performance: 253.773 0.095 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 4 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (12 ms) 60: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There was 1 note 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 2 steps, 0.0 ps. 60: Setting the LD random seed to -256411713 60: 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 192.6 60: (ns/day) (hour/ns) 60: Performance: 153.208 0.157 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Setting nsteps to 4 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 2 60: Runtime for the run 0.002 ps 60: Run end step 2 60: Run end time 0.002 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 4 60: Runtime for the run 0.004 ps 60: Run end step 4 60: Run end time 0.004 ps 60: 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 194.5 60: (ns/day) (hour/ns) 60: Performance: 257.195 0.093 60: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (15 ms) 60: [----------] 6 tests from MdrunTerminationTest (1562 ms total) 60: 60: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 60: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 193.2 60: (ns/day) (hour/ns) 60: Performance: 732.532 0.033 60: trr version: GMX_trn_file (single precision) 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (23 ms) 60: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.013 0.007 198.5 60: (ns/day) (hour/ns) 60: Performance: 223.202 0.108 60: 60: 60: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (28 ms) 60: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (52 ms total) 60: 60: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 190.9 60: (ns/day) (hour/ns) 60: Performance: 748.553 0.032 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.011 0.006 195.7 60: (ns/day) (hour/ns) 60: Performance: 141.019 0.170 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.4 60: (ns/day) (hour/ns) 60: Performance: 509.528 0.047 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (106 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 196.6 60: (ns/day) (hour/ns) 60: Performance: 634.655 0.038 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.045 0.023 199.6 60: (ns/day) (hour/ns) 60: Performance: 34.446 0.697 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: NOTE: 62 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.092 0.046 199.6 60: (ns/day) (hour/ns) 60: Performance: 16.785 1.430 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (163 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 193.9 60: (ns/day) (hour/ns) 60: Performance: 743.046 0.032 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.6 60: (ns/day) (hour/ns) 60: Performance: 509.449 0.047 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.011 0.006 196.8 60: (ns/day) (hour/ns) 60: Performance: 138.994 0.173 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (134 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.036 0.018 199.1 60: (ns/day) (hour/ns) 60: Performance: 81.564 0.294 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 192.6 60: (ns/day) (hour/ns) 60: Performance: 501.922 0.048 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 192.6 60: (ns/day) (hour/ns) 60: Performance: 571.490 0.042 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (66 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.0 60: (ns/day) (hour/ns) 60: Performance: 762.261 0.031 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 190.6 60: (ns/day) (hour/ns) 60: Performance: 540.340 0.044 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.8 60: (ns/day) (hour/ns) 60: Performance: 400.527 0.060 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (36 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.014 0.007 198.3 60: (ns/day) (hour/ns) 60: Performance: 212.317 0.113 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 195.7 60: (ns/day) (hour/ns) 60: Performance: 320.571 0.075 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 194.9 60: (ns/day) (hour/ns) 60: Performance: 439.554 0.055 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (39 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 193.7 60: (ns/day) (hour/ns) 60: Performance: 790.124 0.030 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 191.2 60: (ns/day) (hour/ns) 60: Performance: 531.707 0.045 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.1 60: (ns/day) (hour/ns) 60: Performance: 497.862 0.048 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (39 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 193.6 60: (ns/day) (hour/ns) 60: Performance: 683.296 0.035 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.019 0.010 198.3 60: (ns/day) (hour/ns) 60: Performance: 81.629 0.294 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.012 0.006 197.7 60: (ns/day) (hour/ns) 60: Performance: 126.689 0.189 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (43 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.023 0.011 197.6 60: (ns/day) (hour/ns) 60: Performance: 128.592 0.187 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.015 0.008 197.1 60: (ns/day) (hour/ns) 60: Performance: 103.615 0.232 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.022 0.011 198.2 60: (ns/day) (hour/ns) 60: Performance: 70.260 0.342 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (84 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: NVE simulation: will use the initial temperature of 456.887 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 6 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.010 0.005 195.7 60: (ns/day) (hour/ns) 60: Performance: 273.889 0.088 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 192.7 60: (ns/day) (hour/ns) 60: Performance: 260.690 0.092 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 193.0 60: (ns/day) (hour/ns) 60: Performance: 285.770 0.084 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (77 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.026 0.013 198.7 60: (ns/day) (hour/ns) 60: Performance: 110.150 0.218 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.022 0.011 198.4 60: (ns/day) (hour/ns) 60: Performance: 69.362 0.346 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.014 0.007 197.6 60: (ns/day) (hour/ns) 60: Performance: 111.242 0.216 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (138 ms) 60: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 3 [file unknown]: 60: You are using constraints on all bonds, whereas the forcefield has been 60: parametrized only with constraints involving hydrogen atoms. We suggest 60: using constraints = h-bonds instead, this will also improve performance. 60: 60: Number of degrees of freedom in T-Coupling group System is 23.00 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: There are 9 non-linear virtual site constructions. Their contribution to 60: the energy error is approximated. In most cases this does not affect the 60: error significantly. 60: 60: 60: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 5 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 60: 60: turning all bonds into constraints... 60: 60: Cleaning up constraints and constant bonded interactions with virtual sites 60: 60: Removed 18 Angles with virtual sites, 21 left 60: 60: Removed 10 Proper Dih.s with virtual sites, 44 left 60: 60: Converted 15 Constraints with virtual sites to connections, 7 left 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.027 0.014 198.5 60: (ns/day) (hour/ns) 60: Performance: 107.522 0.223 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 194.3 60: (ns/day) (hour/ns) 60: Performance: 253.202 0.095 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine dipeptide in vacuo' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.015 0.008 197.6 60: (ns/day) (hour/ns) 60: Performance: 101.122 0.237 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (108 ms) 60: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (1039 ms total) 60: 60: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.063 0.031 199.1 60: (ns/day) (hour/ns) 60: Performance: 46.741 0.513 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 192.1 60: (ns/day) (hour/ns) 60: Performance: 269.656 0.089 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 192.2 60: (ns/day) (hour/ns) 60: Performance: 259.157 0.093 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (208 ms) 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 293.480 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.018 0.009 198.8 60: (ns/day) (hour/ns) 60: Performance: 163.824 0.146 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 197.2 60: (ns/day) (hour/ns) 60: Performance: 247.984 0.097 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 193.9 60: (ns/day) (hour/ns) 60: Performance: 251.814 0.095 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (72 ms) 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.024 0.012 198.6 60: (ns/day) (hour/ns) 60: Performance: 119.716 0.200 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.043 0.022 199.0 60: (ns/day) (hour/ns) 60: Performance: 35.670 0.673 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 192.8 60: (ns/day) (hour/ns) 60: Performance: 309.029 0.078 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (143 ms) 60: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.026 0.013 198.5 60: (ns/day) (hour/ns) 60: Performance: 114.032 0.210 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 195.1 60: (ns/day) (hour/ns) 60: Performance: 238.518 0.101 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.014 0.007 197.9 60: (ns/day) (hour/ns) 60: Performance: 106.854 0.225 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (95 ms) 60: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (519 ms total) 60: 60: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.5 60: (ns/day) (hour/ns) 60: Performance: 759.629 0.032 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 189.9 60: (ns/day) (hour/ns) 60: Performance: 533.534 0.045 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.3 60: (ns/day) (hour/ns) 60: Performance: 452.043 0.053 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (62 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 192.3 60: (ns/day) (hour/ns) 60: Performance: 871.248 0.028 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.051 0.026 199.4 60: (ns/day) (hour/ns) 60: Performance: 30.403 0.789 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: NOTE: 56 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.043 0.021 199.4 60: (ns/day) (hour/ns) 60: Performance: 36.316 0.661 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (123 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.8 60: (ns/day) (hour/ns) 60: Performance: 880.462 0.027 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 188.9 60: (ns/day) (hour/ns) 60: Performance: 478.154 0.050 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.5 60: (ns/day) (hour/ns) 60: Performance: 467.463 0.051 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (104 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 196.4 60: (ns/day) (hour/ns) 60: Performance: 617.047 0.039 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.3 60: (ns/day) (hour/ns) 60: Performance: 393.093 0.061 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.8 60: (ns/day) (hour/ns) 60: Performance: 361.705 0.066 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (140 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 196.2 60: (ns/day) (hour/ns) 60: Performance: 617.356 0.039 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 194.2 60: (ns/day) (hour/ns) 60: Performance: 389.060 0.062 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.0 60: (ns/day) (hour/ns) 60: Performance: 367.368 0.065 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (116 ms) 60: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 196.4 60: (ns/day) (hour/ns) 60: Performance: 566.179 0.042 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.1 60: (ns/day) (hour/ns) 60: Performance: 370.203 0.065 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.029 0.014 198.5 60: (ns/day) (hour/ns) 60: Performance: 54.032 0.444 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (98 ms) 60: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (645 ms total) 60: 60: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.1 60: (ns/day) (hour/ns) 60: Performance: 688.796 0.035 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.5 60: (ns/day) (hour/ns) 60: Performance: 507.467 0.047 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.8 60: (ns/day) (hour/ns) 60: Performance: 452.294 0.053 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (75 ms) 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.0 60: (ns/day) (hour/ns) 60: Performance: 742.867 0.032 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.3 60: (ns/day) (hour/ns) 60: Performance: 445.255 0.054 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.7 60: (ns/day) (hour/ns) 60: Performance: 483.973 0.050 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (63 ms) 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 196.5 60: (ns/day) (hour/ns) 60: Performance: 634.851 0.038 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 196.3 60: (ns/day) (hour/ns) 60: Performance: 414.631 0.058 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.027 0.013 198.6 60: (ns/day) (hour/ns) 60: Performance: 57.779 0.415 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (70 ms) 60: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: NVE simulation: will use the initial temperature of 68.810 K for 60: determining the Verlet buffer size 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 196.3 60: (ns/day) (hour/ns) 60: Performance: 713.032 0.034 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.6 60: (ns/day) (hour/ns) 60: Performance: 355.244 0.068 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 193.0 60: (ns/day) (hour/ns) 60: Performance: 386.341 0.062 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (74 ms) 60: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (283 ms total) 60: 60: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.1 60: (ns/day) (hour/ns) 60: Performance: 778.738 0.031 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.1 60: (ns/day) (hour/ns) 60: Performance: 488.540 0.049 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.2 60: (ns/day) (hour/ns) 60: Performance: 506.050 0.047 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (74 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.5 60: (ns/day) (hour/ns) 60: Performance: 782.397 0.031 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 187.8 60: (ns/day) (hour/ns) 60: Performance: 531.707 0.045 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.1 60: (ns/day) (hour/ns) 60: Performance: 478.224 0.050 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (64 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.0 60: (ns/day) (hour/ns) 60: Performance: 749.099 0.032 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 188.5 60: (ns/day) (hour/ns) 60: Performance: 485.847 0.049 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.7 60: (ns/day) (hour/ns) 60: Performance: 460.467 0.052 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (72 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.4 60: (ns/day) (hour/ns) 60: Performance: 789.112 0.030 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.1 60: (ns/day) (hour/ns) 60: Performance: 479.702 0.050 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 191.1 60: (ns/day) (hour/ns) 60: Performance: 482.755 0.050 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (71 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.6 60: (ns/day) (hour/ns) 60: Performance: 802.997 0.030 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 183.4 60: (ns/day) (hour/ns) 60: Performance: 490.893 0.049 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 188.9 60: (ns/day) (hour/ns) 60: Performance: 497.330 0.048 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (71 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.0 60: (ns/day) (hour/ns) 60: Performance: 754.512 0.032 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.1 60: (ns/day) (hour/ns) 60: Performance: 460.208 0.052 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 188.8 60: (ns/day) (hour/ns) 60: Performance: 458.332 0.052 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (111 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.1 60: (ns/day) (hour/ns) 60: Performance: 702.703 0.034 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 188.2 60: (ns/day) (hour/ns) 60: Performance: 448.377 0.054 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.0 60: (ns/day) (hour/ns) 60: Performance: 453.363 0.053 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (107 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.019 0.010 197.5 60: (ns/day) (hour/ns) 60: Performance: 151.403 0.159 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 189.9 60: (ns/day) (hour/ns) 60: Performance: 493.791 0.049 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 198.3 60: (ns/day) (hour/ns) 60: Performance: 78.178 0.307 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (47 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 60: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 191.0 60: (ns/day) (hour/ns) 60: Performance: 717.182 0.033 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.001 188.8 60: (ns/day) (hour/ns) 60: Performance: 544.217 0.044 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 190.4 60: (ns/day) (hour/ns) 60: Performance: 485.702 0.049 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (36 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: 60: WARNING 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There were 2 warnings 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 195.5 60: (ns/day) (hour/ns) 60: Performance: 581.188 0.041 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 196.1 60: (ns/day) (hour/ns) 60: Performance: 383.524 0.063 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 190.6 60: (ns/day) (hour/ns) 60: Performance: 379.773 0.063 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (36 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 196.6 60: (ns/day) (hour/ns) 60: Performance: 575.864 0.042 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.3 60: (ns/day) (hour/ns) 60: Performance: 364.494 0.066 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.5 60: (ns/day) (hour/ns) 60: Performance: 377.487 0.064 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (35 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 60: The Berendsen thermostat does not generate the correct kinetic energy 60: distribution, and should not be used for new production simulations (in 60: our opinion). We would recommend the V-rescale thermostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 196.6 60: (ns/day) (hour/ns) 60: Performance: 567.431 0.042 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.6 60: (ns/day) (hour/ns) 60: Performance: 366.913 0.065 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.4 60: (ns/day) (hour/ns) 60: Performance: 363.559 0.066 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (35 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: 60: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 60: The Berendsen barostat does not generate any strictly correct ensemble, 60: and should not be used for new production simulations (in our opinion). 60: For isotropic scaling we would recommend the C-rescale barostat that also 60: ensures fast relaxation without oscillations, and for anisotropic scaling 60: you likely want to use the Parrinello-Rahman barostat. 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: There was 1 warning 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 196.5 60: (ns/day) (hour/ns) 60: Performance: 563.126 0.043 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.6 60: (ns/day) (hour/ns) 60: Performance: 375.834 0.064 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 189.6 60: (ns/day) (hour/ns) 60: Performance: 337.908 0.071 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (36 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 196.3 60: (ns/day) (hour/ns) 60: Performance: 595.687 0.040 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.9 60: (ns/day) (hour/ns) 60: Performance: 421.490 0.057 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 192.8 60: (ns/day) (hour/ns) 60: Performance: 409.838 0.059 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (35 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 197.2 60: (ns/day) (hour/ns) 60: Performance: 606.596 0.040 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.003 0.002 196.5 60: (ns/day) (hour/ns) 60: Performance: 437.902 0.055 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 193.1 60: (ns/day) (hour/ns) 60: Performance: 419.430 0.057 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (28 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 60: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (0 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 60: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (0 ms) 60: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 197.3 60: (ns/day) (hour/ns) 60: Performance: 599.805 0.040 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 195.8 60: (ns/day) (hour/ns) 60: Performance: 414.842 0.058 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 193.1 60: (ns/day) (hour/ns) 60: Performance: 376.355 0.064 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (36 ms) 60: [----------] 18 tests from NPT/MdrunNoAppendContinuationIsExact (903 ms total) 60: 60: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 60: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Number of degrees of freedom in T-Coupling group System is 33.00 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps. 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 1 of the 1 non-bonded parameter combinations 60: 60: Excluding 1 bonded neighbours molecule type 'Argon' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.007 0.004 195.7 60: (ns/day) (hour/ns) 60: Performance: 397.689 0.060 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 195.0 60: (ns/day) (hour/ns) 60: Performance: 302.859 0.079 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Argon' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.020 0.010 197.7 60: (ns/day) (hour/ns) 60: Performance: 75.900 0.316 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (45 ms) 60: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (45 ms total) 60: 60: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 60: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.021 0.011 197.9 60: (ns/day) (hour/ns) 60: Performance: 138.852 0.173 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 190.4 60: (ns/day) (hour/ns) 60: Performance: 358.366 0.067 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 190.7 60: (ns/day) (hour/ns) 60: Performance: 405.961 0.059 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (51 ms) 60: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'FirstWaterMolecule' has 3 atoms 60: Pull group 2 'SecondWaterMolecule' has 3 atoms 60: Number of degrees of freedom in T-Coupling group System is 9.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 2573.591 K for 60: determining the Verlet buffer size 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 3 2 60: 2 3 5 1.112 nm 1.000 nm 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps. 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 3 of the 3 non-bonded parameter combinations 60: 60: Generated 3 of the 3 1-4 parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.848 nm, buffer size 0.148 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.848 nm, buffer size 0.148 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 196.3 60: (ns/day) (hour/ns) 60: Performance: 475.244 0.051 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.002 195.5 60: (ns/day) (hour/ns) 60: Performance: 333.349 0.072 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc2' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.005 0.003 194.2 60: (ns/day) (hour/ns) 60: Performance: 310.766 0.077 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (44 ms) 60: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (96 ms total) 60: 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: Setting the AWH bias MC random seed to -574644289 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Setting the AWH bias MC random seed to -681841921 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.018 0.009 196.6 60: (ns/day) (hour/ns) 60: Performance: 161.475 0.149 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.006 0.003 190.3 60: (ns/day) (hour/ns) 60: Performance: 230.510 0.104 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.013 0.007 194.6 60: (ns/day) (hour/ns) 60: Performance: 119.281 0.201 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (101 ms) 60: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 60: Setting the AWH bias MC random seed to -8455253 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Setting the AWH bias MC random seed to -1610612931 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: Setting nstcalcenergy (100) equal to nstenergy (4) 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Pull group 1 'C_&_r_1' has 1 atoms 60: Pull group 2 'N_&_r_2' has 1 atoms 60: Pull group 3 'CA' has 1 atoms 60: Pull group 4 'C_&_r_2' has 1 atoms 60: Pull group 5 'N_&_r_3' has 1 atoms 60: Number of degrees of freedom in T-Coupling group System is 51.00 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: Pull group natoms pbc atom distance at start reference at t=0 60: 1 1 0 60: 2 1 0 179.098 deg 0.000 deg 60: 2 1 0 60: 3 1 0 158.667 deg 0.000 deg 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps. 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2145 of the 2145 non-bonded parameter combinations 60: 60: Generated 2145 of the 2145 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.043 0.022 198.4 60: (ns/day) (hour/ns) 60: Performance: 68.170 0.352 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.007 0.003 190.5 60: (ns/day) (hour/ns) 60: Performance: 222.278 0.108 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'Alanine-dipeptide' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: NOTE: 69 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.023 0.012 197.3 60: (ns/day) (hour/ns) 60: Performance: 65.694 0.365 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (119 ms) 60: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (221 ms total) 60: 60: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 60: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 60: that with the Verlet scheme, nstlist has no effect on the accuracy of 60: your simulation. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: Number of degrees of freedom in T-Coupling group System is 79.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps. 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: Generated 2485 of the 2485 non-bonded parameter combinations 60: 60: Generated 2485 of the 2485 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'nonanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 60: 60: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.042 0.021 199.4 60: (ns/day) (hour/ns) 60: Performance: 69.400 0.346 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 8 steps, 0.0 ps. 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.021 0.011 198.7 60: (ns/day) (hour/ns) 60: Performance: 72.101 0.333 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 60: 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun '30 system in water' 60: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.010 0.005 193.5 60: (ns/day) (hour/ns) 60: Performance: 145.356 0.165 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (113 ms) 60: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (113 ms total) 60: 60: [----------] 3 tests from Checking/InitialConstraintsTest 60: [ RUN ] Checking/InitialConstraintsTest.Works/0 60: Number of degrees of freedom in T-Coupling group rest is 11.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 60: NVE simulation: will use the initial temperature of 1141.954 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc-and-methanol' 60: 1 steps, 0.0 ps. 60: Setting the LD random seed to 2145316570 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: NOTE: 10 % of the run time was spent in pair search, 60: you might want to increase nstlist (this has no effect on accuracy) 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 188.8 60: (ns/day) (hour/ns) 60: Performance: 132.452 0.181 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (9 ms) 60: [ RUN ] Checking/InitialConstraintsTest.Works/1 60: Number of degrees of freedom in T-Coupling group rest is 11.00 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 60: NVE simulation: will use the initial temperature of 1141.954 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 2 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc-and-methanol' 60: 1 steps, 0.0 ps. 60: Setting the LD random seed to 938913011 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.004 0.002 194.3 60: (ns/day) (hour/ns) 60: Performance: 95.290 0.252 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (9 ms) 60: [ RUN ] Checking/InitialConstraintsTest.Works/2 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 60: Integrator method md-vv-avek is implemented primarily for validation 60: purposes; for molecular dynamics, you should probably be using md or md-vv 60: 60: Number of degrees of freedom in T-Coupling group rest is 11.00 60: 60: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 60: NVE simulation: will use the initial temperature of 1141.954 K for 60: determining the Verlet buffer size 60: 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 3 notes 60: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 60: log). 60: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 60: Can not increase nstlist because an NVE ensemble is used 60: Using 1 MPI process 60: Using 2 OpenMP threads 60: 60: 60: NOTE: The number of threads is not equal to the number of (logical) cpus 60: and the -pin option is set to auto: will not pin threads to cpus. 60: This can lead to significant performance degradation. 60: Consider using -pin on (and -pinoffset in case you run multiple jobs). 60: starting mdrun 'spc-and-methanol' 60: 1 steps, 0.0 ps. 60: Setting the LD random seed to -83902601 60: 60: Generated 8 of the 10 non-bonded parameter combinations 60: 60: Excluding 2 bonded neighbours molecule type 'Methanol' 60: 60: turning H bonds into constraints... 60: 60: Excluding 2 bonded neighbours molecule type 'SOL' 60: 60: turning H bonds into constraints... 60: 60: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 60: 60: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 60: 60: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 60: 60: Note that mdrun will redetermine rlist based on the actual pair-list setup 60: 60: This run will generate roughly 0 Mb of data 60: 60: Writing final coordinates. 60: 60: Core t (s) Wall t (s) (%) 60: Time: 0.002 0.001 186.0 60: (ns/day) (hour/ns) 60: Performance: 135.980 0.176 60: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 60: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (9 ms) 60: [----------] 3 tests from Checking/InitialConstraintsTest (28 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 66 tests from 13 test suites ran. (7394 ms total) 60: [ PASSED ] 66 tests. 60/81 Test #60: MdrunIOTests ................................... Passed 8.56 sec test 61 Start 61: MdrunTestsOneRank 61: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunTestsOneRank.xml" 61: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 61: Test timeout computed to be: 600 61: [==========] Running 22 tests from 6 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from CompelTest 61: [ RUN ] CompelTest.SwapCanRun 61: Setting the LD random seed to -277087233 61: 61: Generated 330891 of the 330891 non-bonded parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 330891 of the 330891 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein' 61: 61: turning all bonds into constraints... 61: 61: Excluding 3 bonded neighbours molecule type 'OCT' 61: 61: turning all bonds into constraints... 61: 61: Excluding 1 bonded neighbours molecule type 'NA' 61: 61: turning all bonds into constraints... 61: 61: Excluding 1 bonded neighbours molecule type 'CL' 61: 61: turning all bonds into constraints... 61: 61: Excluding 3 bonded neighbours molecule type 'Protein' 61: 61: Excluding 3 bonded neighbours molecule type 'OCT' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: turning all bonds into constraints... 61: Split0 group 'Ch0' contains 83 atoms. 61: Split1 group 'Ch1' contains 83 atoms. 61: Solvent group 'SOL' contains 11931 atoms. 61: Swap group 'NA+' contains 19 atoms. 61: Swap group 'CL-' contains 19 atoms. 61: Number of degrees of freedom in T-Coupling group System is 27869.00 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 61: Removing center of mass motion in the presence of position restraints 61: might cause artifacts. When you are using position restraints to 61: equilibrate a macro-molecule, the artifacts are usually negligible. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 notes 61: 61: This run will generate roughly 1 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: SWAP: Determining initial numbers of ions per compartment. 61: SWAP: Setting pointers for checkpoint writing 61: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 61: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 61: starting mdrun 'Channel_coco in octane membrane' 61: 2 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: NOTE: 43 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.621 0.311 199.9 61: (ns/day) (hour/ns) 61: Performance: 4.169 5.756 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 61: 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: SWAP: Setting pointers for checkpoint writing 61: SWAP: Copying channel fluxes from checkpoint file data 61: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 61: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 61: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 61: starting mdrun 'Channel_coco in octane membrane' 61: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 61: 61: Writing final coordinates. 61: 61: NOTE: 29 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.431 0.216 199.9 61: (ns/day) (hour/ns) 61: Performance: 6.007 3.995 61: [ OK ] CompelTest.SwapCanRun (1385 ms) 61: [----------] 1 test from CompelTest (1385 ms total) 61: 61: [----------] 6 tests from BondedInteractionsTest 61: [ RUN ] BondedInteractionsTest.NormalBondWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Setting the LD random seed to -6570019 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 2 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 24 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.001 192.5 61: (ns/day) (hour/ns) 61: Performance: 164.051 0.146 61: [ OK ] BondedInteractionsTest.NormalBondWorks (7 ms) 61: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Setting the LD random seed to -741352481 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 2 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 25 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.001 193.8 61: (ns/day) (hour/ns) 61: Performance: 129.842 0.185 61: [ OK ] BondedInteractionsTest.TabulatedBondWorks (8 ms) 61: [ RUN ] BondedInteractionsTest.NormalAngleWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Setting the LD random seed to -173061 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: This run will generate roughly 0 Mb of data 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 25 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.001 193.3 61: (ns/day) (hour/ns) 61: Performance: 160.349 0.150 61: [ OK ] BondedInteractionsTest.NormalAngleWorks (7 ms) 61: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Setting the LD random seed to -101195799 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: This run will generate roughly 0 Mb of data 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 26 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.001 192.8 61: (ns/day) (hour/ns) 61: Performance: 169.896 0.141 61: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (8 ms) 61: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: Setting the LD random seed to -135467525 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: 61: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: There were 3 notes 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 31 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.001 193.9 61: (ns/day) (hour/ns) 61: Performance: 137.216 0.175 61: [ OK ] BondedInteractionsTest.NormalDihedralWorks (8 ms) 61: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 61: For a correct single-point energy evaluation with nsteps = 0, use 61: continuation = yes to avoid constraining the input coordinates. 61: 61: 61: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 61: In moleculetype 'butane' 4 atoms are not bound by a potential or 61: constraint to any other atom in the same moleculetype. Although 61: technically this might not cause issues in a simulation, this often means 61: that the user forgot to add a bond/potential/constraint or put multiple 61: molecules in the same moleculetype definition by mistake. Run with -v to 61: get information for each atom. 61: 61: Setting the LD random seed to 2008547167 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'butane' 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 61: NVE simulation with an initial temperature of zero: will use a Verlet 61: buffer of 10%. Check your energy drift! 61: 61: 61: This run will generate roughly 0 Mb of data 61: 61: There were 3 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 61: 61: Reading frames from gro file 'A single butane', 4 atoms. 61: Reading frame 0 time 0.000 Last frame 0 time 0.000 61: 61: NOTE: 32 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.001 0.001 193.3 61: (ns/day) (hour/ns) 61: Performance: 156.471 0.153 61: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (9 ms) 61: [----------] 6 tests from BondedInteractionsTest (51 ms total) 61: 61: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 61: Setting the LD random seed to -108678 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: This run will generate roughly 0 Mb of data 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.014 0.007 196.5 61: (ns/day) (hour/ns) 61: Performance: 59.375 0.404 61: Setting the LD random seed to -1914751233 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: This run will generate roughly 0 Mb of data 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.012 0.006 195.9 61: (ns/day) (hour/ns) 61: Performance: 70.561 0.340 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 61: 61: 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (485 ms) 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 61: Setting the LD random seed to -607200501 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: There were 2 notes 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.014 0.007 196.8 61: (ns/day) (hour/ns) 61: Performance: 59.384 0.404 61: Setting the LD random seed to -67634507 61: 61: Generated 2211 of the 2211 non-bonded parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 2211 of the 2211 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 61: 61: turning H bonds into constraints... 61: 61: NOTE 1 [file ala.top, line 256]: 61: For energy conservation with LINCS, lincs_iter should be 2 or larger. 61: 61: 61: Number of degrees of freedom in T-Coupling group rest is 54.00 61: 61: The largest distance between excluded atoms is 0.384 nm 61: Calculating fourier grid dimensions for X Y Z 61: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 61: The optimal PME mesh load for parallel simulations is below 0.5 61: and for highly parallel simulations between 0.25 and 0.33, 61: for higher performance, increase the cut-off and the PME grid spacing. 61: 61: 61: 61: There were 2 notes 61: 61: Estimate for the relative computational load of the PME mesh part: 0.94 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 61: Can not increase nstlist because an NVE ensemble is used 61: 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'UNNAMED in water' 61: 4 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.012 0.006 196.2 61: (ns/day) (hour/ns) 61: Performance: 72.094 0.333 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 61: 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (68 ms) 61: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (553 ms total) 61: 61: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 61: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 61: Setting the LD random seed to -604359169 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: turning H bonds into constraints... 61: Pull group 1 'FirstWaterMolecule' has 3 atoms 61: Pull group 2 'SecondWaterMolecule' has 3 atoms 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: Pull group natoms pbc atom distance at start reference at t=0 61: 1 3 2 61: 2 3 5 1.112 nm 1.000 nm 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'spc2' 61: 4 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.005 0.003 191.7 61: (ns/day) (hour/ns) 61: Performance: 164.647 0.146 61: Setting the LD random seed to -107219150 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: turning H bonds into constraints... 61: Pull group 1 'FirstWaterMolecule' has 3 atoms 61: Pull group 2 'SecondWaterMolecule' has 3 atoms 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: Pull group natoms pbc atom distance at start reference at t=0 61: 1 3 2 61: 2 3 5 1.112 nm 1.000 nm 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 61: Can not increase nstlist because an NVE ensemble is used 61: 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'spc2' 61: 4 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.006 0.003 193.2 61: (ns/day) (hour/ns) 61: Performance: 140.286 0.171 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 61: 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 61: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 61: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (25 ms) 61: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (25 ms total) 61: 61: [----------] 8 tests from FreezeWorks/FreezeGroupTest 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: NVE simulation: will use the initial temperature of 318.937 K for 61: determining the Verlet buffer size 61: 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 5 notes 61: 61: There was 1 warning 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.008 0.004 192.5 61: (ns/day) (hour/ns) 61: Performance: 189.094 0.127 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (25 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 61: 61: 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: NVE simulation: will use the initial temperature of 318.937 K for 61: determining the Verlet buffer size 61: 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: This run will generate roughly 0 Mb of data 61: 61: There were 5 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.008 0.004 192.9 61: (ns/day) (hour/ns) 61: Performance: 181.325 0.132 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (25 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: NVE simulation: will use the initial temperature of 318.937 K for 61: determining the Verlet buffer size 61: 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 5 notes 61: 61: There was 1 warning 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.010 0.005 195.9 61: (ns/day) (hour/ns) 61: Performance: 159.229 0.151 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (25 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 61: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 61: Parrinello-Rahman is not implemented in md-vv. 61: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (0 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 notes 61: 61: There was 1 warning 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 61: 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.009 0.005 196.1 61: (ns/day) (hour/ns) 61: Performance: 165.853 0.145 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (27 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 61: 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.010 0.005 195.2 61: (ns/day) (hour/ns) 61: Performance: 159.074 0.151 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (28 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: This run will generate roughly 0 Mb of data 61: 61: There were 4 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 61: 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.008 0.004 195.7 61: (ns/day) (hour/ns) 61: Performance: 192.532 0.125 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (30 ms) 61: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generated 2145 of the 2145 non-bonded parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Generated 2145 of the 2145 1-4 parameter combinations 61: 61: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 61: 61: turning H bonds into constraints... 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: There are 5 atoms that are fully frozen and part of COMM removal 61: group(s), removing these atoms from the COMM removal group(s) 61: 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: There are 3 atoms that are frozen along less then 3 dimensions and part 61: of COMM removal group(s), due to limitations in the code these still 61: contribute to the mass of the COM along frozen dimensions and therefore 61: the COMM correction will be too small. 61: 61: Number of degrees of freedom in T-Coupling group System is 25.50 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 4 notes 61: 61: There was 1 warning 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 61: 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'Alanine-dipeptide' 61: 8 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.009 0.005 194.4 61: (ns/day) (hour/ns) 61: Performance: 166.990 0.144 61: 61: 61: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (30 ms) 61: [----------] 8 tests from FreezeWorks/FreezeGroupTest (194 ms total) 61: 61: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to 2139078335 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: This run will generate roughly 0 Mb of data 61: 61: There were 2 notes 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.006 0.003 193.1 61: (ns/day) (hour/ns) 61: Performance: 517.820 0.046 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (11 ms) 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to -1149376513 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: There were 2 notes 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because verlet-buffer-tolerance is not set or used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.006 0.003 193.5 61: (ns/day) (hour/ns) 61: Performance: 512.129 0.047 61: 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (11 ms) 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: There were 2 notes 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to -70522882 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (11 ms) 61: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.007 0.004 194.4 61: (ns/day) (hour/ns) 61: Performance: 442.776 0.054 61: 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Generating 1-4 interactions: fudge = 0.5 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Setting gen_seed to -206995969 61: 61: Velocities were taken from a Maxwell distribution at 0 K 61: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 61: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 61: Net Acceleration in X direction, will not be corrected 61: Net Acceleration in Y direction, will not be corrected 61: Net Acceleration in Z direction, will not be corrected 61: 61: There were 2 notes 61: 61: This run will generate roughly 0 Mb of data 61: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 61: log). 61: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 61: Can not increase nstlist because verlet-buffer-tolerance is not set or used 61: Using 1 MPI process 61: 61: Non-default thread affinity set, disabling internal thread affinity 61: 61: Using 2 OpenMP threads 61: 61: starting mdrun 'spc2' 61: 8 steps, 0.0 ps. 61: 61: Writing final coordinates. 61: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (12 ms) 61: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (47 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 22 tests from 6 test suites ran. (2866 ms total) 61: [ PASSED ] 21 tests. 61: [ SKIPPED ] 1 test, listed below: 61: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.007 0.004 194.8 61: (ns/day) (hour/ns) 61: Performance: 436.466 0.055 61: 61/81 Test #61: MdrunTestsOneRank .............................. Passed 3.40 sec test 62 Start 62: MdrunTestsTwoRanks 62: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunTestsTwoRanks.xml" 62: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 62: Test timeout computed to be: 600 62: [==========] Running 22 tests from 6 test suites. 62: [----------] Global test environment set-up. 62: [----------] 1 test from CompelTest 62: [ RUN ] CompelTest.SwapCanRun 62: Setting the LD random seed to -541135437 62: 62: Generated 330891 of the 330891 non-bonded parameter combinations 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Generated 330891 of the 330891 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein' 62: 62: turning all bonds into constraints... 62: 62: Excluding 3 bonded neighbours molecule type 'OCT' 62: 62: turning all bonds into constraints... 62: 62: Excluding 1 bonded neighbours molecule type 'NA' 62: 62: turning all bonds into constraints... 62: 62: Excluding 1 bonded neighbours molecule type 'CL' 62: 62: turning all bonds into constraints... 62: 62: Excluding 3 bonded neighbours molecule type 'Protein' 62: 62: Excluding 3 bonded neighbours molecule type 'OCT' 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: turning all bonds into constraints... 62: Split0 group 'Ch0' contains 83 atoms. 62: Split1 group 'Ch1' contains 83 atoms. 62: Solvent group 'SOL' contains 11931 atoms. 62: Swap group 'NA+' contains 19 atoms. 62: Swap group 'CL-' contains 19 atoms. 62: Number of degrees of freedom in T-Coupling group System is 27869.00 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 62: Removing center of mass motion in the presence of position restraints 62: might cause artifacts. When you are using position restraints to 62: equilibrate a macro-molecule, the artifacts are usually negligible. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: This run will generate roughly 1 Mb of data 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: SWAP: Determining initial numbers of ions per compartment. 62: SWAP: Setting pointers for checkpoint writing 62: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 62: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 62: starting mdrun 'Channel_coco in octane membrane' 62: 2 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 1.0%. 62: The balanceable part of the MD step is 19%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.2%. 62: 62: 62: NOTE: 6 % of the run time was spent in domain decomposition, 62: 34 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.949 0.237 399.7 62: (ns/day) (hour/ns) 62: Performance: 5.459 4.396 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 62: 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: SWAP: Setting pointers for checkpoint writing 62: SWAP: Copying channel fluxes from checkpoint file data 62: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 62: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 62: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 62: starting mdrun 'Channel_coco in octane membrane' 62: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 62: 62: Writing final coordinates. 62: 62: NOTE: 25 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.655 0.164 399.7 62: (ns/day) (hour/ns) 62: Performance: 7.913 3.033 62: [ OK ] CompelTest.SwapCanRun (1918 ms) 62: [----------] 1 test from CompelTest (1918 ms total) 62: 62: [----------] 6 tests from BondedInteractionsTest 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: [ RUN ] BondedInteractionsTest.NormalBondWorks 62: Setting the LD random seed to -9240609 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 2 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: 62: This run will generate roughly 0 Mb of data 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 25 % of the run time was spent in domain decomposition, 62: 20 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.003 0.001 386.8 62: (ns/day) (hour/ns) 62: Performance: 113.548 0.211 62: [ OK ] BondedInteractionsTest.NormalBondWorks (17 ms) 62: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Setting the LD random seed to -813695169 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 2 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: This run will generate roughly 0 Mb of data 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 29 % of the run time was spent in domain decomposition, 62: 20 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.003 0.001 388.0 62: (ns/day) (hour/ns) 62: Performance: 123.597 0.194 62: [ OK ] BondedInteractionsTest.TabulatedBondWorks (9 ms) 62: [ RUN ] BondedInteractionsTest.NormalAngleWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Setting the LD random seed to 1744559855 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: This run will generate roughly 0 Mb of data 62: 62: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 27 % of the run time was spent in domain decomposition, 62: 23 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.003 0.001 386.7 62: (ns/day) (hour/ns) 62: Performance: 113.601 0.211 62: [ OK ] BondedInteractionsTest.NormalAngleWorks (8 ms) 62: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Setting the LD random seed to -1658851848 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: This run will generate roughly 0 Mb of data 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 26 % of the run time was spent in domain decomposition, 62: 24 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.003 0.001 387.4 62: (ns/day) (hour/ns) 62: Performance: 111.009 0.216 62: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (8 ms) 62: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Setting the LD random seed to 1811660221 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: This run will generate roughly 0 Mb of data 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 [ OK ] BondedInteractionsTest.NormalDihedralWorks (8 ms) 62: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 62: Last frame 0 time 0.000 62: 62: NOTE: 27 % of the run time was spent in domain decomposition, 62: 18 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.003 0.001 389.4 62: (ns/day) (hour/ns) 62: Performance: 110.754 0.217 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Setting the LD random seed to -67109121 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'butane' 62: 62: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 62: In moleculetype 'butane' 4 atoms are not bound by a potential or 62: constraint to any other atom in the same moleculetype. Although 62: technically this might not cause issues in a simulation, this often means 62: that the user forgot to add a bond/potential/constraint or put multiple 62: molecules in the same moleculetype definition by mistake. Run with -v to 62: get information for each atom. 62: 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: This run will generate roughly 0 Mb of data 62: 62: There were 3 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/butane1.gro' 62: 62: Reading frames from gro file 'A single butane', 4 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 26 % of the run time was spent in domain decomposition, 62: 20 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.003 0.001 388.0 62: (ns/day) (hour/ns) 62: Performance: 106.852 0.225 62: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (9 ms) 62: [----------] 6 tests from BondedInteractionsTest (62 ms total) 62: 62: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 62: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 62: Setting the LD random seed to 2079104382 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: This run will generate roughly 0 Mb of data 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.055 0.014 395.9 62: (ns/day) (hour/ns) 62: Performance: 30.887 0.777 62: Setting the LD random seed to -1107297825 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: This run will generate roughly 0 Mb of data 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: NOTE: 10 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.023 0.006 391.4 62: (ns/day) (hour/ns) 62: Performance: 74.310 0.323 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: 62: 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 62: 62: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (451 ms) 62: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 62: Setting the LD random seed to 917227647 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: This run will generate roughly 0 Mb of data 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: NOTE: 8 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.026 0.007 392.6 62: (ns/day) (hour/ns) 62: Performance: 64.407 0.373 62: Setting the LD random seed to 1538129912 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: turning H bonds into constraints... 62: 62: NOTE 1 [file ala.top, line 256]: 62: For energy conservation with LINCS, lincs_iter should be 2 or larger. 62: 62: 62: Number of degrees of freedom in T-Coupling group rest is 54.00 62: 62: The largest distance between excluded atoms is 0.384 nm 62: Calculating fourier grid dimensions for X Y Z 62: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 62: 62: Estimate for the relative computational load of the PME mesh part: 0.94 62: 62: This run will generate roughly 0 Mb of data 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 62: The optimal PME mesh load for parallel simulations is below 0.5 62: and for highly parallel simulations between 0.25 and 0.33, 62: for higher performance, increase the cut-off and the PME grid spacing. 62: 62: 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 62: Can not increase nstlist because an NVE ensemble is used 62: 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'UNNAMED in water' 62: 4 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: NOTE: 10 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.023 0.006 389.8 62: (ns/day) (hour/ns) 62: Performance: 73.679 0.326 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 62: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 62: 62: 62: 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 62: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (65 ms) 62: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (516 ms total) 62: 62: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 62: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 62: Setting the LD random seed to -187465809 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: turning H bonds into constraints... 62: Pull group 1 'FirstWaterMolecule' has 3 atoms 62: Pull group 2 'SecondWaterMolecule' has 3 atoms 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: Pull group natoms pbc atom distance at start reference at t=0 62: 1 3 2 62: 2 3 5 1.112 nm 1.000 nm 62: 62: This run will generate roughly 0 Mb of data 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'spc2' 62: 4 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: NOTE: 18 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.012 0.003 383.0 62: (ns/day) (hour/ns) 62: Performance: 137.696 0.174 62: Setting the LD random seed to -42035246 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: turning H bonds into constraints... 62: Pull group 1 'FirstWaterMolecule' has 3 atoms 62: Pull group 2 'SecondWaterMolecule' has 3 atoms 62: Number of degrees of freedom in T-Coupling group rest is 9.00 62: Pull group natoms pbc atom distance at start reference at t=0 62: 1 3 2 62: 2 3 5 1.112 nm 1.000 nm 62: 62: This run will generate roughly 0 Mb of data 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 62: Can not increase nstlist because an NVE ensemble is used 62: 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'spc2' 62: 4 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: NOTE: 18 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.012 0.003 382.7 62: (ns/day) (hour/ns) 62: Performance: 135.008 0.178 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 62: 62: 62: 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 62: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 62: Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (25 ms) 62: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (26 ms total) 62: 62: [----------] 8 tests from FreezeWorks/FreezeGroupTest 62: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: NVE simulation: will use the initial temperature of 318.937 K for 62: determining the Verlet buffer size 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: This run will generate roughly 0 Mb of data 62: 62: There were 5 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 3.8%. 62: The balanceable part of the MD step is 67%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 2.5%. 62: 62: 62: NOTE: 13 % of the run time was spent in domain decomposition, 62: 6 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 10 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.019 0.005 391.4 62: (ns/day) (hour/ns) 62: Performance: 158.776 0.151 62: 62: 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (26 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: NVE simulation: will use the initial temperature of 318.937 K for 62: determining the Verlet buffer size 62: 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: This run will generate roughly 0 Mb of data 62: 62: There were 5 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 4.1%. 62: The balanceable part of the MD step is 68%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 2.8%. 62: 62: 62: NOTE: 11 % of the run time was spent in domain decomposition, 62: 5 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 11 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.019 0.005 386.3 62: (ns/day) (hour/ns) 62: Performance: 156.814 0.153 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (26 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: NVE simulation: will use the initial temperature of 318.937 K for 62: determining the Verlet buffer size 62: 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 5 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 0.5%. 62: The balanceable part of the MD step is 72%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.4%. 62: 62: 62: NOTE: 13 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.022 0.006 390.4 62: (ns/day) (hour/ns) 62: Performance: 136.799 0.175 62: 62: 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (26 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 62: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (0 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 notes 62: 62: There was 1 warning 62: 62: This run will generate roughly 0 Mb of data 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 62: 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: NOTE: 10 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.021 0.005 392.4 62: (ns/day) (hour/ns) 62: Performance: 142.336 0.169 62: 62: 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (29 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.749 nm, buffer size 0.049 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.747 nm, buffer size 0.047 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 notes 62: 62: There was 1 warning 62: 62: This run will generate roughly 0 Mb of data 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Changing nstlist from 8 to 25, rlist from 0.747 to 0.875 62: 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: NOTE: 10 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.021 0.005 391.7 62: (ns/day) (hour/ns) 62: Performance: 144.451 0.166 62: 62: 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (29 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 4 notes 62: 62: There was 1 warning 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 62: 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: NOTE: 10 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.017 0.004 389.3 62: (ns/day) (hour/ns) 62: Performance: 175.907 0.136 62: 62: 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (30 ms) 62: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Generated 2145 of the 2145 non-bonded parameter combinations 62: 62: Generated 2145 of the 2145 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 62: 62: turning H bonds into constraints... 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: There are 5 atoms that are fully frozen and part of COMM removal 62: group(s), removing these atoms from the COMM removal group(s) 62: 62: 62: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: There are 3 atoms that are frozen along less then 3 dimensions and part 62: of COMM removal group(s), due to limitations in the code these still 62: contribute to the mass of the COM along frozen dimensions and therefore 62: the COMM correction will be too small. 62: 62: Number of degrees of freedom in T-Coupling group System is 25.50 62: 62: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 62: 62: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: This run will generate roughly 0 Mb of data 62: 62: There were 4 notes 62: 62: There was 1 warning 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 62: 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'Alanine-dipeptide' 62: 8 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: NOTE: 10 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.018 0.005 390.6 62: (ns/day) (hour/ns) 62: Performance: 167.574 0.143 62: 62: 62: 62: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (30 ms) 62: [----------] 8 tests from FreezeWorks/FreezeGroupTest (198 ms total) 62: 62: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 62: 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to -1085804609 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: This run will generate roughly 0 Mb of data 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 0.5%. 62: The balanceable part of the MD step is 70%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.3%. 62: 62: 62: NOTE: 12 % of the run time was spent in domain decomposition, 62: 7 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 13 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.014 0.004 380.4 62: (ns/day) (hour/ns) 62: Performance: 423.942 0.057 62: 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (12 ms) 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to -444941444 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: There were 2 notes 62: 62: This run will generate roughly 0 Mb of data 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because verlet-buffer-tolerance is not set or used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 0.1%. 62: The balanceable part of the MD step is 70%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.1%. 62: 62: 62: NOTE: 12 % of the run time was spent in domain decomposition, 62: 7 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 11 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.015 0.004 390.4 62: (ns/day) (hour/ns) 62: Performance: 402.753 0.060 62: 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (12 ms) 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generated 3 of the 3 1-4 parameter combinations 62: Generating 1-4 interactions: fudge = 0.5 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to -714114177 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: There were 2 notes 62: 62: This run will generate roughly 0 Mb of data 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 0.4%. 62: The balanceable part of the MD step is 71%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.3%. 62: 62: 62: NOTE: 11 % of the run time was spent in domain decomposition, 62: 6 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 10 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.017 0.004 391.2 62: (ns/day) (hour/ns) 62: Performance: 351.094 0.068 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (12 ms) 62: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 62: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 62: that with the Verlet scheme, nstlist has no effect on the accuracy of 62: your simulation. 62: 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (4) 62: 62: Generated 3 of the 3 non-bonded parameter combinations 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Generated 3 of the 3 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: Setting gen_seed to 2046115829 62: 62: Velocities were taken from a Maxwell distribution at 0 K 62: 62: This run will generate roughly 0 Mb of data 62: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 62: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 62: Net Acceleration in X direction, will not be corrected 62: Net Acceleration in Y direction, will not be corrected 62: Net Acceleration in Z direction, will not be corrected 62: 62: There were 2 notes 62: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 62: log). 62: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 62: Can not increase nstlist because verlet-buffer-tolerance is not set or used 62: Using 2 MPI processes 62: 62: Non-default thread affinity set, disabling internal thread affinity 62: 62: Using 2 OpenMP threads per MPI process 62: 62: starting mdrun 'spc2' 62: 8 steps, 0.0 ps. 62: 62: Writing final coordinates. 62: 62: 62: Dynamic load balancing report: 62: DLB was off during the run due to low measured imbalance. 62: Average load imbalance: 0.1%. 62: The balanceable part of the MD step is 73%, load imbalance is computed from this. 62: Part of the total run time spent waiting due to load imbalance: 0.1%. 62: 62: 62: NOTE: 10 % of the run time was spent in domain decomposition, 62: 6 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: NOTE: 10 % of the run time was spent communicating energies, 62: you might want to increase some nst* mdp options 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.017 0.004 390.2 62: (ns/day) (hour/ns) 62: Performance: 367.388 0.065 62: 62: 62: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (12 ms) 62: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (51 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 22 tests from 6 test suites ran. (3327 ms total) 62: [ PASSED ] 21 tests. 62: [ SKIPPED ] 1 test, listed below: 62: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 62/81 Test #62: MdrunTestsTwoRanks ............................. Passed 3.87 sec test 63 Start 63: MdrunSingleRankAlgorithmsTests 63: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 63: Test timeout computed to be: 600 63: [==========] Running 4 tests from 2 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from OriresTest 63: [ RUN ] OriresTest.OriresCanRun 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 518.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 note 63: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 63: log). 63: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 63: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 63: 10 steps, 0.0 ps. 63: Setting the LD random seed to 834587260 63: 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.013 0.006 196.8 63: (ns/day) (hour/ns) 63: Performance: 298.586 0.080 63: [ OK ] OriresTest.OriresCanRun (275 ms) 63: [----------] 1 test from OriresTest (275 ms total) 63: 63: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 63: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 63: Number of degrees of freedom in T-Coupling group rest is 10.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 63: The optimal PME mesh load for parallel simulations is below 0.5 63: and for highly parallel simulations between 0.25 and 0.33, 63: for higher performance, increase the cut-off and the PME grid spacing. 63: 63: 63: 63: There were 2 notes 63: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 63: log). 63: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Dipoles' 63: 20 steps, 0.1 ps. 63: Setting the LD random seed to -1228931739 63: 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Dipole' 63: 63: Searching the wall atom type(s) 63: 63: The largest distance between excluded atoms is 0.344 nm 63: Calculating fourier grid dimensions for X Y Z 63: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 63: 63: Estimate for the relative computational load of the PME mesh part: 1.00 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.031 0.016 198.5 63: (ns/day) (hour/ns) 63: Performance: 290.792 0.083 63: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 63: 63: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (788 ms) 63: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 63: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 63: The supported numbers are > 1. 63: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 63: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: With epsilon_surface > 0 all molecules should be neutral. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: With epsilon_surface > 0 you can only use domain decomposition when there 63: are only small molecules with all bonds constrained (mdrun will check for 63: this). 63: 63: Number of degrees of freedom in T-Coupling group rest is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: NVE simulation with an initial temperature of zero: will use a Verlet 63: buffer of 10%. Check your energy drift! 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 63: The optimal PME mesh load for parallel simulations is below 0.5 63: and for highly parallel simulations between 0.25 and 0.33, 63: for higher performance, increase the cut-off and the PME grid spacing. 63: 63: 63: 63: There were 4 notes 63: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 63: log). 63: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Dipoles' 63: 20 steps, 0.1 ps. 63: Setting the LD random seed to 666595251 63: 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Dipole' 63: 63: The largest distance between excluded atoms is 0.344 nm 63: Calculating fourier grid dimensions for X Y Z 63: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 63: 63: Estimate for the relative computational load of the PME mesh part: 1.00 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.015 0.008 197.6 63: (ns/day) (hour/ns) 63: Performance: 588.274 0.041 63: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 63: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (282 ms) 63: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (1071 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 4 tests from 2 test suites ran. (1500 ms total) 63: [ PASSED ] 4 tests. 63/81 Test #63: MdrunSingleRankAlgorithmsTests ................. Passed 2.00 sec test 64 Start 64: MdrunNonIntegratorTests 64: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunNonIntegratorTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 58 tests from 5 test suites. 64: [----------] Global test environment set-up. 64: [----------] 1 test from NonbondedBenchTest 64: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 64: SIMD width: 4 64: System size: 3000 atoms 64: Cut-off radius: 1 nm 64: Number of threads: 1 64: Number of iterations: 1 64: Compute energies: no 64: Ewald excl. corr.: analytical 64: 64: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 64: total useful 64: Ewald all geom. 4xM 21.704 21.7035 0.0548 0.0290 64: [ OK ] NonbondedBenchTest.BasicEndToEndTest (28 ms) 64: [----------] 1 test from NonbondedBenchTest (28 ms total) 64: 64: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -4.7991024e+01 64: Maximum force = 1.8629706e+02 on atom 13 64: Norm of force = 8.7721851e+01 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (594 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 3.02331e+02 on atom 3 64: F-Norm = 1.18024e+02 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -5.5862484e+01 64: Maximum force = 4.2726132e+02 on atom 13 64: Norm of force = 1.8452547e+02 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (556 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 22.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 3.1937714e+02 64: Maximum force = 9.9988643e+03 on atom 9 64: Norm of force = 4.6166996e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (134 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: 64: NOTE 3 [file glycine_vacuo.top, line 12]: 64: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 64: 64: Number of degrees of freedom in T-Coupling group System is 22.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 2.41575e+04 on atom 10 64: F-Norm = 1.18451e+04 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 1.5174426e+02 64: Maximum force = 7.4208862e+03 on atom 9 64: Norm of force = 3.5692992e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (134 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -1.5698444e+02 64: Maximum force = 4.5699695e+02 on atom 17 64: Norm of force = 1.8327127e+02 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (22 ms) 64: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: 64: NOTE 4 [file unknown]: 64: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 1.06802e+03 on atom 28 64: F-Norm = 4.26922e+02 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -1.6941083e+02 64: Maximum force = 2.1829454e+02 on atom 17 64: Norm of force = 7.9205749e+01 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (23 ms) 64: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1465 ms total) 64: 64: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents converged to Fmax < 10 in 1 steps 64: Potential Energy = -9.7425687e-01 64: Maximum force = 4.0132279e+00 on atom 1 64: Norm of force = 1.6383933e+00 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (8 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 4.01323e+00 on atom 1 64: F-Norm = 1.63839e+00 64: 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 64: Potential Energy = -9.9064195e-01 64: Maximum force = 2.5781672e+00 on atom 1 64: Norm of force = 1.0525324e+00 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (8 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 64: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: 64: There was 1 warning 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Low-Memory BFGS Minimizer: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: Using 10 BFGS correction steps. 64: 64: F-max = 4.01323e+00 on atom 1 64: F-Norm = 1.63839e+00 64: 64: 64: writing lowest energy coordinates. 64: 64: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 64: Potential Energy = -9.9064195e-01 64: Maximum force = 2.5781672e+00 on atom 1 64: Norm of force = 1.0525324e+00 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (9 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 3.1939697e+02 64: Maximum force = 9.9704248e+03 on atom 9 64: Norm of force = 4.6227540e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (135 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Polak-Ribiere Conjugate Gradients: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: F-max = 2.41672e+04 on atom 10 64: F-Norm = 1.19357e+04 64: 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = 1.5625757e+02 64: Maximum force = 7.5018242e+03 on atom 9 64: Norm of force = 3.6139019e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (133 ms) 64: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 64: setting nstcomm equal to nstcalcenergy for less overhead 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 64: 64: Generating 1-4 interactions: fudge = 1 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: 64: There was 1 warning 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Low-Memory BFGS Minimizer: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: Using 10 BFGS correction steps. 64: 64: F-max = 2.41672e+04 on atom 10 64: F-Norm = 1.19357e+04 64: 64: 64: Energy minimization has stopped, but the forces have not converged to the 64: requested precision Fmax < 10 (which may not be possible for your system). It 64: stopped because the algorithm tried to make a new step whose size was too 64: small, or there was no change in the energy since last step. Either way, we 64: regard the minimization as converged to within the available machine 64: precision, given your starting configuration and EM parameters. 64: 64: Double precision normally gives you higher accuracy, but this is often not 64: needed for preparing to run molecular dynamics. 64: 64: writing lowest energy coordinates. 64: 64: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 64: but did not reach the requested Fmax < 10. 64: Potential Energy = 5.6111731e+02 64: Maximum force = 1.2685497e+04 on atom 10 64: Norm of force = 6.0643635e+03 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (133 ms) 64: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (428 ms total) 64: 64: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 192.2 64: (ns/day) (hour/ns) 64: Performance: 757.295 0.032 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 64: 64: trr version: GMX_trn_file (single precision) 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 195.0 64: (ns/day) (hour/ns) 64: Performance: 1711.276 0.014 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (14 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.002 197.1 64: (ns/day) (hour/ns) 64: Performance: 631.144 0.038 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 194.1 64: (ns/day) (hour/ns) 64: Performance: 2133.170 0.011 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (14 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 192.3 64: (ns/day) (hour/ns) 64: Performance: 831.614 0.029 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 194.2 64: (ns/day) (hour/ns) 64: Performance: 1956.365 0.012 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (14 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Number of degrees of freedom in T-Coupling group System is 33.00 64: 64: There were 2 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 16 steps, 0.0 ps. 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 193.2 64: (ns/day) (hour/ns) 64: Performance: 885.397 0.027 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 194.8 64: (ns/day) (hour/ns) 64: Performance: 1902.592 0.013 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (13 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: NVE simulation: will use the initial temperature of 398.997 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 192.4 64: (ns/day) (hour/ns) 64: Performance: 686.188 0.035 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 23 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 194.1 64: (ns/day) (hour/ns) 64: Performance: 1751.164 0.014 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (541 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: NVE simulation: will use the initial temperature of 398.997 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.003 195.8 64: (ns/day) (hour/ns) 64: Performance: 545.572 0.044 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 194.1 64: (ns/day) (hour/ns) 64: Performance: 1746.695 0.014 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (534 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 192.9 64: (ns/day) (hour/ns) 64: Performance: 752.117 0.032 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 194.2 64: (ns/day) (hour/ns) 64: Performance: 1669.085 0.014 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (422 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 16 steps, 0.0 ps. 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 192.7 64: (ns/day) (hour/ns) 64: Performance: 688.411 0.035 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.001 0.001 194.6 64: (ns/day) (hour/ns) 64: Performance: 1936.685 0.012 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (412 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: NVE simulation: will use the initial temperature of 456.887 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 6 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.008 0.004 194.7 64: (ns/day) (hour/ns) 64: Performance: 370.161 0.065 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 195.0 64: (ns/day) (hour/ns) 64: Performance: 1146.797 0.021 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (30 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: NVE simulation: will use the initial temperature of 456.887 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 6 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 6 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.008 0.004 195.5 64: (ns/day) (hour/ns) 64: Performance: 342.769 0.070 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 11 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 194.8 64: (ns/day) (hour/ns) 64: Performance: 782.397 0.031 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (32 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.008 0.004 195.2 64: (ns/day) (hour/ns) 64: Performance: 372.286 0.064 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.002 0.001 194.4 64: (ns/day) (hour/ns) 64: Performance: 1223.797 0.020 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (52 ms) 64: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file unknown]: 64: You are using constraints on all bonds, whereas the forcefield has been 64: parametrized only with constraints involving hydrogen atoms. We suggest 64: using constraints = h-bonds instead, this will also improve performance. 64: 64: Number of degrees of freedom in T-Coupling group System is 23.00 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: There are 9 non-linear virtual site constructions. Their contribution to 64: the energy error is approximated. In most cases this does not affect the 64: error significantly. 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine dipeptide in vacuo' 64: 16 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 64: 64: turning all bonds into constraints... 64: 64: Cleaning up constraints and constant bonded interactions with virtual sites 64: 64: Removed 18 Angles with virtual sites, 21 left 64: 64: Removed 10 Proper Dih.s with virtual sites, 44 left 64: 64: Converted 15 Constraints with virtual sites to connections, 7 left 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 194.0 64: (ns/day) (hour/ns) 64: Performance: 301.842 0.080 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 23 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 195.5 64: (ns/day) (hour/ns) 64: Performance: 1028.136 0.023 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (46 ms) 64: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2130 ms total) 64: 64: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.007 0.003 193.7 64: (ns/day) (hour/ns) 64: Performance: 426.398 0.056 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.005 0.002 193.0 64: (ns/day) (hour/ns) 64: Performance: 605.107 0.040 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (33 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.007 0.004 180.0 64: (ns/day) (hour/ns) 64: Performance: 365.310 0.066 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 194.6 64: (ns/day) (hour/ns) 64: Performance: 1001.885 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (32 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.007 0.004 194.0 64: (ns/day) (hour/ns) 64: Performance: 395.544 0.061 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.5 64: (ns/day) (hour/ns) 64: Performance: 946.182 0.025 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (31 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.008 0.004 192.5 64: (ns/day) (hour/ns) 64: Performance: 347.840 0.069 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.6 64: (ns/day) (hour/ns) 64: Performance: 940.405 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (32 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.008 0.004 189.7 64: (ns/day) (hour/ns) 64: Performance: 368.567 0.065 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 16 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 193.2 64: (ns/day) (hour/ns) 64: Performance: 983.492 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (31 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 195.2 64: (ns/day) (hour/ns) 64: Performance: 281.769 0.085 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 850.206 0.028 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (33 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.007 0.004 190.9 64: (ns/day) (hour/ns) 64: Performance: 393.774 0.061 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 887.950 0.027 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (31 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 193.8 64: (ns/day) (hour/ns) 64: Performance: 324.772 0.074 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.6 64: (ns/day) (hour/ns) 64: Performance: 899.357 0.027 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (32 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 194.5 64: (ns/day) (hour/ns) 64: Performance: 309.453 0.078 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 195.5 64: (ns/day) (hour/ns) 64: Performance: 823.389 0.029 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (33 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.007 0.004 192.9 64: (ns/day) (hour/ns) 64: Performance: 398.951 0.060 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 194.5 64: (ns/day) (hour/ns) 64: Performance: 1002.048 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (31 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.007 0.004 193.7 64: (ns/day) (hour/ns) 64: Performance: 398.744 0.060 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 194.3 64: (ns/day) (hour/ns) 64: Performance: 1043.991 0.023 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (31 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.005 197.7 64: (ns/day) (hour/ns) 64: Performance: 276.483 0.087 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 192.2 64: (ns/day) (hour/ns) 64: Performance: 930.463 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (33 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.006 195.9 64: (ns/day) (hour/ns) 64: Performance: 265.063 0.091 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 793.891 0.030 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (33 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.005 196.8 64: (ns/day) (hour/ns) 64: Performance: 267.480 0.090 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 193.5 64: (ns/day) (hour/ns) 64: Performance: 929.060 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (34 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.012 0.006 196.6 64: (ns/day) (hour/ns) 64: Performance: 240.217 0.100 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 193.4 64: (ns/day) (hour/ns) 64: Performance: 740.901 0.032 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (34 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 197.5 64: (ns/day) (hour/ns) 64: Performance: 286.579 0.084 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 194.5 64: (ns/day) (hour/ns) 64: Performance: 990.449 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (32 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 197.6 64: (ns/day) (hour/ns) 64: Performance: 293.599 0.082 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 193.9 64: (ns/day) (hour/ns) 64: Performance: 991.405 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (32 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.005 196.7 64: (ns/day) (hour/ns) 64: Performance: 270.012 0.089 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.9 64: (ns/day) (hour/ns) 64: Performance: 856.233 0.028 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (33 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 195.6 64: (ns/day) (hour/ns) 64: Performance: 273.962 0.088 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.4 64: (ns/day) (hour/ns) 64: Performance: 919.492 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (33 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.012 0.006 197.1 64: (ns/day) (hour/ns) 64: Performance: 239.488 0.100 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.001 193.8 64: (ns/day) (hour/ns) 64: Performance: 1001.560 0.024 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (33 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 197.4 64: (ns/day) (hour/ns) 64: Performance: 296.910 0.081 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 193.9 64: (ns/day) (hour/ns) 64: Performance: 910.253 0.026 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (32 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: NVE simulation: will use the initial temperature of 293.480 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.005 197.7 64: (ns/day) (hour/ns) 64: Performance: 274.732 0.087 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.1 64: (ns/day) (hour/ns) 64: Performance: 959.744 0.025 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (33 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.004 192.5 64: (ns/day) (hour/ns) 64: Performance: 330.451 0.073 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 195.1 64: (ns/day) (hour/ns) 64: Performance: 832.288 0.029 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (52 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 192.5 64: (ns/day) (hour/ns) 64: Performance: 319.500 0.075 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 194.9 64: (ns/day) (hour/ns) 64: Performance: 763.773 0.031 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (49 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 195.1 64: (ns/day) (hour/ns) 64: Performance: 294.202 0.082 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 744.213 0.032 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (50 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 193.8 64: (ns/day) (hour/ns) 64: Performance: 315.604 0.076 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 195.0 64: (ns/day) (hour/ns) 64: Performance: 856.947 0.028 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (50 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.004 195.0 64: (ns/day) (hour/ns) 64: Performance: 330.274 0.073 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 21 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 194.2 64: (ns/day) (hour/ns) 64: Performance: 755.067 0.032 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (50 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 195.5 64: (ns/day) (hour/ns) 64: Performance: 312.625 0.077 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 28 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 195.3 64: (ns/day) (hour/ns) 64: Performance: 767.580 0.031 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (49 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.004 191.9 64: (ns/day) (hour/ns) 64: Performance: 331.339 0.072 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 13 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 838.861 0.029 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (48 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.008 0.004 191.6 64: (ns/day) (hour/ns) 64: Performance: 333.113 0.072 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 194.4 64: (ns/day) (hour/ns) 64: Performance: 703.023 0.034 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (49 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.008 0.004 194.9 64: (ns/day) (hour/ns) 64: Performance: 348.687 0.069 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.7 64: (ns/day) (hour/ns) 64: Performance: 884.253 0.027 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (48 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 196.0 64: (ns/day) (hour/ns) 64: Performance: 302.687 0.079 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.003 0.002 194.5 64: (ns/day) (hour/ns) 64: Performance: 960.791 0.025 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (49 ms) 64: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group System is 79.00 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 notes 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun '30 system in water' 64: 16 steps, 0.0 ps. 64: Generated 2485 of the 2485 non-bonded parameter combinations 64: 64: Generated 2485 of the 2485 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'nonanol' 64: 64: turning H bonds into constraints... 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.010 0.005 195.7 64: (ns/day) (hour/ns) 64: Performance: 290.334 0.083 64: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 64: log). 64: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 64: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 64: 64: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.004 0.002 193.4 64: (ns/day) (hour/ns) 64: Performance: 757.016 0.032 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 64: 64: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (48 ms) 64: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (1274 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 58 tests from 5 test suites ran. (5650 ms total) 64: [ PASSED ] 58 tests. 64/81 Test #64: MdrunNonIntegratorTests ........................ Passed 6.19 sec test 65 Start 65: MdrunTpiTests 65: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunTpiTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 2 tests from 1 test suite. 65: [----------] Global test environment set-up. 65: [----------] 2 tests from Simple/TpiTest 65: [ RUN ] Simple/TpiTest.ReproducesOutput/0 65: Ignoring obsolete mdp entry 'ns_type' 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 1308.00 65: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 65: log). 65: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 65: TPI is not implemented for GPUs. 65: 65: Using 1 MPI process 65: Using 1 OpenMP thread 65: 65: 65: NOTE: Thread affinity was not set. 65: Reading frames from gro file '216 water molecules', 648 atoms. 65: Reading frame 0 time 0.000 mu 3.905e+02 3.905e+02 65: Last frame 0 time 0.000 65: Generated 331705 of the 331705 non-bonded parameter combinations 65: 65: Generated 331705 of the 331705 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Excluding 3 bonded neighbours molecule type 'methane' 65: Analysing residue names: 65: There are: 216 Water residues 65: There are: 1 Other residues 65: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] Simple/TpiTest.ReproducesOutput/0 (483 ms) 65: [ RUN ] Simple/TpiTest.ReproducesOutput/1 65: Ignoring obsolete mdp entry 'ns_type' 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 1308.00 65: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 65: log). 65: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 65: TPI is not implemented for GPUs. 65: 65: Using 1 MPI process 65: Using 1 OpenMP thread 65: 65: 65: NOTE: Thread affinity was not set. 65: Reading frames from gro file '216 water molecules', 648 atoms. 65: Reading frame 0 time 0.000 mu 1.070e+02 1.070e+02 65: Last frame 0 time 0.000 65: Generated 331705 of the 331705 non-bonded parameter combinations 65: 65: Generated 331705 of the 331705 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Excluding 3 bonded neighbours molecule type 'methane' 65: Analysing residue names: 65: There are: 216 Water residues 65: There are: 1 Other residues 65: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] Simple/TpiTest.ReproducesOutput/1 (474 ms) 65: [----------] 2 tests from Simple/TpiTest (958 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 2 tests from 1 test suite ran. (1039 ms total) 65: [ PASSED ] 2 tests. 65/81 Test #65: MdrunTpiTests .................................. Passed 1.60 sec test 66 Start 66: MdrunMpiTests 66: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMpiTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 17 tests from 4 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from DomainDecompositionSpecialCasesTest 66: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Setting the LD random seed to -33923586 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: starting mdrun 'spc2' 66: 0 steps, 0.0 ps. 66: 66: NOTE: 29 % of the run time was spent in domain decomposition, 66: 16 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: NOTE: 6 % of the run time was spent communicating energies, 66: you might want to increase some nst* mdp options 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 346.4 66: (ns/day) (hour/ns) 66: Performance: 109.931 0.218 66: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (10 ms) 66: [----------] 1 test from DomainDecompositionSpecialCasesTest (10 ms total) 66: 66: [----------] 4 tests from MimicTest 66: [ RUN ] MimicTest.OneQuantumMol 66: Setting the LD random seed to 1974956903 66: 66: Generated 10 of the 10 non-bonded parameter combinations 66: 66: Generated 10 of the 10 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 21.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: [ OK ] MimicTest.OneQuantumMol (8 ms) 66: [ RUN ] MimicTest.AllQuantumMol 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 66: 66: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 34 % of the run time was spent in domain decomposition, 66: 16 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: NOTE: 6 % of the run time was spent communicating energies, 66: you might want to increase some nst* mdp options 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 388.0 66: (ns/day) (hour/ns) 66: Performance: 102.009 0.235 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group rest is 21.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Setting the LD random seed to 1610604527 66: 66: Generated 10 of the 10 non-bonded parameter combinations 66: 66: Generated 10 of the 10 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 66: 66: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 66: Reading frame 0 time 0.000 [ OK ] MimicTest.AllQuantumMol (9 ms) 66: [ RUN ] MimicTest.TwoQuantumMol 66: Last frame 0 time 0.000 66: 66: NOTE: 31 % of the run time was spent in domain decomposition, 66: 14 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 388.7 66: (ns/day) (hour/ns) 66: Performance: 96.405 0.249 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Setting the LD random seed to -1456538665 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 10 of the 10 non-bonded parameter combinations 66: 66: Generated 10 of the 10 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: Number of degrees of freedom in T-Coupling group rest is 21.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/4water.gro' 66: 66: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 29 % of the run time was spent in domain decomposition, 66: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.003 0.001 386.9 66: (ns/day) (hour/ns) 66: Performance: 123.787 0.194 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.TwoQuantumMol (9 ms) 66: [ RUN ] MimicTest.BondCuts 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Setting the LD random seed to -557908265 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2211 of the 2211 non-bonded parameter combinations 66: 66: Generated 2211 of the 2211 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Number of degrees of freedom in T-Coupling group rest is 66.00 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 66: NVE simulation: will use the initial temperature of 300.368 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/ala.gro' 66: 66: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 27 % of the run time was spent in domain decomposition, 66: 16 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.004 0.001 389.8 66: (ns/day) (hour/ns) 66: Performance: 85.986 0.279 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.BondCuts (22 ms) 66: [----------] 4 tests from MimicTest (50 ms total) 66: 66: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generated 330891 of the 330891 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 330891 of the 330891 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: This run will generate roughly 0 Mb of data 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -4.7991013e+01 66: Maximum force = 1.8629756e+02 on atom 13 66: Norm of force = 8.7722025e+01 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (489 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generated 330891 of the 330891 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 330891 of the 330891 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: 66: This run will generate roughly 0 Mb of data 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 3.02331e+02 on atom 3 66: F-Norm = 1.18024e+02 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -5.5862144e+01 66: Maximum force = 4.2727667e+02 on atom 13 66: Norm of force = 1.8453053e+02 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (429 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generated 20503 of the 20503 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 1 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: turning H bonds into constraints... 66: Number of degrees of freedom in T-Coupling group System is 22.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 3.1937704e+02 66: Maximum force = 9.9988633e+03 on atom 9 66: Norm of force = 4.6166993e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (140 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generated 20503 of the 20503 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 1 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file glycine_vacuo.top, line 12]: 66: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 66: 66: Number of degrees of freedom in T-Coupling group System is 22.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 notes 66: 66: This run will generate roughly 0 Mb of data 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 2.41575e+04 on atom 10 66: F-Norm = 1.18451e+04 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 1.5174426e+02 66: Maximum force = 7.4208862e+03 on atom 9 66: Norm of force = 3.5692992e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (129 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 notes 66: 66: This run will generate roughly 0 Mb of data 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -1.5698450e+02 66: Maximum force = 4.5699695e+02 on atom 17 66: Norm of force = 1.8326839e+02 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (23 ms) 66: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning all bonds into constraints... 66: 66: NOTE 3 [file unknown]: 66: You are using constraints on all bonds, whereas the forcefield has been 66: parametrized only with constraints involving hydrogen atoms. We suggest 66: using constraints = h-bonds instead, this will also improve performance. 66: 66: 66: NOTE 4 [file unknown]: 66: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 66: 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 15 Constraints with virtual sites to connections, 7 left 66: Number of degrees of freedom in T-Coupling group System is 23.00 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 5 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 1.06802e+03 on atom 28 66: F-Norm = 4.26922e+02 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = -1.6941113e+02 66: Maximum force = 2.1830547e+02 on atom 17 66: Norm of force = 7.9205267e+01 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (27 ms) 66: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1242 ms total) 66: 66: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 2 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents converged to Fmax < 10 in 1 steps 66: Potential Energy = -9.7425687e-01 66: Maximum force = 4.0132279e+00 on atom 3 66: Norm of force = 1.6383933e+00 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (17 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: This run will generate roughly 0 Mb of data 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 4.01323e+00 on atom 3 66: F-Norm = 1.63839e+00 66: 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 66: Potential Energy = -9.9064195e-01 66: Maximum force = 2.5781672e+00 on atom 3 66: Norm of force = 1.0525324e+00 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (8 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 66: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: Number of degrees of freedom in T-Coupling group System is 33.00 66: 66: There were 2 notes 66: 66: There was 1 warning 66: 66: This run will generate roughly 0 Mb of data 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (4 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generated 20503 of the 20503 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 1 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 3 notes 66: 66: This run will generate roughly 0 Mb of data 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: 66: Steepest Descents: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Steepest Descents did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 3.1939685e+02 66: Maximum force = 9.9704248e+03 on atom 9 66: Norm of force = 4.6227568e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (126 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: Generated 20503 of the 20503 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 1 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 3 notes 66: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 66: log). 66: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 66: Using 2 MPI processes 66: 66: Non-default thread affinity set, disabling internal thread affinity 66: 66: Using 2 OpenMP threads per MPI process 66: 66: 66: Polak-Ribiere Conjugate Gradients: 66: Tolerance (Fmax) = 1.00000e+01 66: Number of steps = 4 66: F-max = 2.41672e+04 on atom 10 66: F-Norm = 1.19357e+04 66: 66: 66: Energy minimization reached the maximum number of steps before the forces 66: reached the requested precision Fmax < 10. 66: 66: writing lowest energy coordinates. 66: 66: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 66: Potential Energy = 1.5625761e+02 66: Maximum force = 7.5018237e+03 on atom 9 66: Norm of force = 3.6139019e+03 66: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (126 ms) 66: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 66: setting nstcomm equal to nstcalcenergy for less overhead 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 66: 66: Generated 20503 of the 20503 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 1 66: 66: Generated 17396 of the 20503 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Glycine' 66: Number of degrees of freedom in T-Coupling group System is 27.00 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 3 notes 66: 66: There was 1 warning 66: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (118 ms) 66: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (402 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 17 tests from 4 test suites ran. (2068 ms total) 66: [ PASSED ] 17 tests. 66/81 Test #66: MdrunMpiTests .................................. Passed 2.59 sec test 67 Start 67: MdrunMultiSimTests 67: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-multisim-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMultiSimTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 6 tests from 2 test suites. 67: [----------] Global test environment set-up. 67: [----------] 4 tests from InNvt/MultiSimTest 67: [ RUN ] InNvt/MultiSimTest.ExitsNormally/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: Setting the LD random seed to -43286831 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: Setting the LD random seed to -445288463 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 2080374746 67: 67: Velocities were taken from a Maxwell distribution at 278 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Setting the LD random seed to -1644171593 67: Setting the LD random seed to -415254539 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -69207041 67: 67: Velocities were taken from a Maxwell distribution at 268 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Setting gen_seed to -1415628713 67: 67: Velocities were taken from a Maxwell distribution at 288 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Setting gen_seed to -539496306 67: 67: Velocities were taken from a Maxwell distribution at 298 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: This is simulation 3 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 2 steps, 0.0 ps. 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 67: log). 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: This is simulation 0 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 2 steps, 0.0 ps. 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: This is simulation 1 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 2 steps, 0.0 ps. 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: This is simulation 2 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 2 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: Writing final coordinates. 67: 67: Writing final coordinates. 67: 67: Writing final coordinates. 67: [ OK ] InNvt/MultiSimTest.ExitsNormally/0 (16 ms) 67: [ RUN ] InNvt/MultiSimTest.ExitsNormally/1 67: Setting the LD random seed to -548669833 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -16846862 67: 67: Velocities were taken from a Maxwell distribution at 278 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Setting the LD random seed to -302038273 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: This is simulation 1 out of 2 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 2 MPI processes 67: Using 1 OpenMP thread per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 2 steps, 0.0 ps. 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 67: log). 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: This is simulation 0 out of 2 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 2 MPI processes 67: Using 1 OpenMP thread per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 2 steps, 0.0 ps. 67: 67: Setting gen_seed to 1457102580 67: 67: Velocities were taken from a Maxwell distribution at 298 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Writing final coordinates. 67: 67: NOTE: 34 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Writing final coordinates. 67: 67: NOTE: 35 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: [ OK ] InNvt/MultiSimTest.ExitsNormally/1 (10 ms) 67: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 67: Setting the LD random seed to -294551553 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -13172995 67: 67: Velocities were taken from a Maxwell distribution at 288 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Setting the LD random seed to 2147407286 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -738468361 67: 67: Velocities were taken from a Maxwell distribution at 278 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Setting the LD random seed to -6375724 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 1475965931 67: 67: Velocities were taken from a Maxwell distribution at 298 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Setting the LD random seed to -1094722577 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -190447682 67: 67: Velocities were taken from a Maxwell distribution at 268 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 notes 67: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 67: log). 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: This is simulation 0 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: This is simulation 2 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: This is simulation 3 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: This is simulation 1 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: Using 1 OpenMP thread 67: 67: Using 1 OpenMP thread 67: 67: Using 1 OpenMP thread 67: 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 1 steps, 0.0 ps. 67: starting mdrun 'spc2' 67: 2 steps, 0.0 ps. 67: starting mdrun 'spc2' 67: 3 steps, 0.0 ps. 67: starting mdrun 'spc2' 67: 0 steps, 0.0 ps. 67: 67: Note: The number of steps is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: Note: The number of steps is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: Note: The number of steps is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: Note: The number of steps is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: NOTE: 12 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Writing final coordinates. 67: 67: Writing final coordinates. 67: 67: Writing final coordinates. 67: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 (10 ms) 67: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Setting the LD random seed to -273163009 67: Setting the LD random seed to -273154106 67: Generating 1-4 interactions: fudge = 0.5 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: 67: Setting gen_seed to -1411393857 67: 67: Velocities were taken from a Maxwell distribution at 278 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: Setting gen_seed to 1056696319 67: 67: Velocities were taken from a Maxwell distribution at 298 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 3 notes 67: 67: This run will generate roughly 0 Mb of data 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 67: log). 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: This is simulation 0 out of 2 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 2 MPI processes 67: Using 1 OpenMP thread per MPI process 67: 67: This is simulation 1 out of 2 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 2 MPI processes 67: Using 1 OpenMP thread per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 1 steps, 0.0 ps. 67: starting mdrun 'spc2' 67: 0 steps, 0.0 ps. 67: 67: Note: The number of steps is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: Note: The number of steps is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: NOTE: 32 % of the run time was spent in domain decomposition, 67: 10 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 6 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Writing final coordinates. 67: 67: NOTE: 10 % of the run time was spent in domain decomposition, 67: 3 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 32 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 (9 ms) 67: [----------] 4 tests from InNvt/MultiSimTest (49 ms total) 67: 67: [----------] 2 tests from InNvt/MultiSimTerminationTest 67: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 67: Setting the LD random seed to -1133666633 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 2141052923 67: 67: Velocities were taken from a Maxwell distribution at 298 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: Setting the LD random seed to 1996095103 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Setting the LD random seed to -786449 67: Setting the LD random seed to 1798567356 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: 67: This run will generate roughly 0 Mb of data 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 2145353136 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Velocities were taken from a Maxwell distribution at 268 K 67: 67: Setting gen_seed to -68714993 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: Velocities were taken from a Maxwell distribution at 278 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: 67: Setting gen_seed to -8802322 67: 67: Velocities were taken from a Maxwell distribution at 288 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: This run will generate roughly 0 Mb of data 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: 67: This run will generate roughly 0 Mb of data 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: 67: This run will generate roughly 0 Mb of data 67: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 67: log). 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 67: 67: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 67: 67: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 67: 67: This is simulation 0 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 100 steps, 0.1 ps. 67: This is simulation 3 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 100 steps, 0.1 ps. 67: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 67: 67: This is simulation 1 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 100 steps, 0.1 ps. 67: This is simulation 2 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 100 steps, 0.1 ps. 67: 67: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps 67: 67: Step 2: Run time exceeded 0.000 hours, will terminate the run within 2 steps 67: 67: Step 2: Run time exceeded 0.000 hours, will terminate the run within 2 steps 67: 67: Step 3: Run time exceeded 0.000 hours, will terminate the run within 2 steps 67: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 67: log). 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 67: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 67: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: 67: This is simulation 1 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 67: 67: Note: The initial step is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: Writing final coordinates. 67: 67: This is simulation 0 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Note: The initial step is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: Writing final coordinates. 67: 67: This is simulation 2 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 5 steps, 0.0 ps (continuing from step 3, 0.0 ps). 67: 67: Note: The initial step is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: Writing final coordinates. 67: 67: This is simulation 3 out of 4 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 1 MPI process 67: Using 1 OpenMP thread 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 5 steps, 0.0 ps (continuing from step 3, 0.0 ps). 67: 67: Note: The initial step is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: Writing final coordinates. 67: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (15 ms) 67: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 67: You have set rlist larger than the interaction cut-off, but you also have 67: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Setting the LD random seed to -238465 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: Setting the LD random seed to -257993153 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -684265497 67: 67: Velocities were taken from a Maxwell distribution at 278 K 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: Setting gen_seed to -138702858 67: 67: Velocities were taken from a Maxwell distribution at 298 K 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: Number of degrees of freedom in T-Coupling group System is 9.00 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 2 notes 67: 67: This run will generate roughly 0 Mb of data 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 67: 67: This is simulation 1 out of 2 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 2 MPI processes 67: Using 1 OpenMP thread per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 100 steps, 0.1 ps. 67: 67: Step 2: Run time exceeded 0.000 hours, will terminate the run within 2 steps 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 2.7%. 67: The balanceable part of the MD step is 20%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 0.5%. 67: 67: 67: NOTE: 20 % of the run time was spent in domain decomposition, 67: 5 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 27 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 67: log). 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 67: 67: This is simulation 0 out of 2 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 2 MPI processes 67: Using 1 OpenMP thread per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 100 steps, 0.1 ps. 67: 67: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 6.3%. 67: The balanceable part of the MD step is 22%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 1.4%. 67: 67: 67: NOTE: 19 % of the run time was spent in domain decomposition, 67: 5 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 28 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 67: log). 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 67: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 67: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 67: 67: 67: This is simulation 0 out of 2 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 2 MPI processes 67: 67: This is simulation 1 out of 2 running as a composite GROMACS 67: multi-simulation job. Setup for this simulation: 67: 67: Using 2 MPI processes 67: Using 1 OpenMP thread per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Note: The initial step is not consistent across multi simulations, 67: but we are proceeding anyway! 67: Using 1 OpenMP thread per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 5 steps, 0.0 ps (continuing from step 3, 0.0 ps). 67: 67: Note: The initial step is not consistent across multi simulations, 67: but we are proceeding anyway! 67: 67: Writing final coordinates. 67: 67: Writing final coordinates. 67: 67: NOTE: 38 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: NOTE: 36 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (14 ms) 67: [----------] 2 tests from InNvt/MultiSimTerminationTest (31 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 6 tests from 2 test suites ran. (308 ms total) 67: [ PASSED ] 6 tests. 67/81 Test #67: MdrunMultiSimTests ............................. Passed 0.80 sec test 68 Start 68: MdrunMultiSimReplexTests 68: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-multisim-replex-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMultiSimReplexTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 5 tests from 2 test suites. 68: [----------] Global test environment set-up. 68: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest 68: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: Setting the LD random seed to -139206737 68: Generating 1-4 interactions: fudge = 0.5 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: Setting the LD random seed to -268740675 68: 68: Setting gen_seed to -553926697 68: 68: Velocities were taken from a Maxwell distribution at 298 K 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: Generating 1-4 interactions: fudge = 0.5 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: Setting the LD random seed to -873341069 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: 68: This run will generate roughly 0 Mb of data 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: Setting the LD random seed to -9078273 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Setting gen_seed to -211293317 68: 68: Velocities were taken from a Maxwell distribution at 278 K 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: Generating 1-4 interactions: fudge = 0.5 68: 68: Setting gen_seed to -905974593 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: Velocities were taken from a Maxwell distribution at 268 K 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: 68: This run will generate roughly 0 Mb of data 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: Setting gen_seed to -1481396513 68: 68: Velocities were taken from a Maxwell distribution at 288 K 68: 68: This run will generate roughly 0 Mb of data 68: 68: There were 2 notes 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: 68: This run will generate roughly 0 Mb of data 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 68: log). 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: This is simulation 0 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: This is simulation 3 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: This is simulation 2 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: This is simulation 1 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 (22 ms) 68: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: The Berendsen barostat does not generate any strictly correct ensemble, 68: and should not be used for new production simulations (in our opinion). 68: For isotropic scaling we would recommend the C-rescale barostat that also 68: ensures fast relaxation without oscillations, and for anisotropic scaling 68: you likely want to use the Parrinello-Rahman barostat. 68: 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: The Berendsen barostat does not generate any strictly correct ensemble, 68: and should not be used for new production simulations (in our opinion). 68: For isotropic scaling we would recommend the C-rescale barostat that also 68: ensures fast relaxation without oscillations, and for anisotropic scaling 68: you likely want to use the Parrinello-Rahman barostat. 68: 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: The Berendsen barostat does not generate any strictly correct ensemble, 68: and should not be used for new production simulations (in our opinion). 68: For isotropic scaling we would recommend the C-rescale barostat that also 68: ensures fast relaxation without oscillations, and for anisotropic scaling 68: you likely want to use the Parrinello-Rahman barostat. 68: 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: The Berendsen barostat does not generate any strictly correct ensemble, 68: and should not be used for new production simulations (in our opinion). 68: For isotropic scaling we would recommend the C-rescale barostat that also 68: ensures fast relaxation without oscillations, and for anisotropic scaling 68: you likely want to use the Parrinello-Rahman barostat. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Setting the LD random seed to -571212241 68: Setting the LD random seed to 399501087 68: Setting the LD random seed to -539789701 68: Setting the LD random seed to -824246925 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: Generating 1-4 interactions: fudge = 0.5 68: Generating 1-4 interactions: fudge = 0.5 68: Generating 1-4 interactions: fudge = 0.5 68: 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to 1308616437 68: 68: Velocities were taken from a Maxwell distribution at 268 K 68: 68: Setting gen_seed to -168042509 68: 68: Velocities were taken from a Maxwell distribution at 288 K 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Setting gen_seed to -67412993 68: 68: Velocities were taken from a Maxwell distribution at 278 K 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Setting gen_seed to -92836919 68: 68: Velocities were taken from a Maxwell distribution at 298 K 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: 68: There was 1 warning 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: 68: There was 1 warning 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: 68: There was 1 warning 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: 68: There was 1 warning 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 68: log). 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: This is simulation 0 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: This is simulation 1 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: This is simulation 3 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: This is simulation 2 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 (11 ms) 68: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: Setting the LD random seed to -34365988 68: Generating 1-4 interactions: fudge = 0.5 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: Setting the LD random seed to 720632821 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Setting gen_seed to 1070006263 68: 68: Velocities were taken from a Maxwell distribution at 278 K 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: This run will generate roughly 0 Mb of data 68: 68: There were 2 notes 68: 68: Setting gen_seed to -40730956 68: 68: Velocities were taken from a Maxwell distribution at 298 K 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 68: log). 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: This is simulation 0 out of 2 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 2 MPI processes 68: This is simulation 1 out of 2 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 2 MPI processes 68: Using 1 OpenMP thread per MPI process 68: 68: Using 1 OpenMP thread per MPI process 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 34.7%. 68: The balanceable part of the MD step is 30%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 10.3%. 68: 68: NOTE: 10.3 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 11.2%. 68: The balanceable part of the MD step is 21%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 2.3%. 68: 68: 68: NOTE: 12 % of the run time was spent in domain decomposition, 68: 3 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 32 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: NOTE: 12 % of the run time was spent in domain decomposition, 68: 5 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 32 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 (11 ms) 68: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 68: The Berendsen barostat does not generate any strictly correct ensemble, 68: and should not be used for new production simulations (in our opinion). 68: For isotropic scaling we would recommend the C-rescale barostat that also 68: ensures fast relaxation without oscillations, and for anisotropic scaling 68: you likely want to use the Parrinello-Rahman barostat. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 68: The Berendsen barostat does not generate any strictly correct ensemble, 68: and should not be used for new production simulations (in our opinion). 68: For isotropic scaling we would recommend the C-rescale barostat that also 68: ensures fast relaxation without oscillations, and for anisotropic scaling 68: you likely want to use the Parrinello-Rahman barostat. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Setting the LD random seed to -1226978372 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -138617026 68: 68: Velocities were taken from a Maxwell distribution at 278 K 68: Setting the LD random seed to -1075970093 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: 68: There was 1 warning 68: 68: This run will generate roughly 0 Mb of data 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: 68: There was 1 warning 68: 68: Setting gen_seed to -1226344453 68: 68: Velocities were taken from a Maxwell distribution at 298 K 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 68: log). 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: This is simulation 1 out of 2 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 2 MPI processes 68: Using 1 OpenMP thread per MPI process 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: This is simulation 0 out of 2 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 2 MPI processes 68: Using 1 OpenMP thread per MPI process 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: starting mdrun 'spc2' 68: 2 steps, 0.0 ps. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 33.4%. 68: The balanceable part of the MD step is 30%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 10.1%. 68: 68: NOTE: 10.1 % of the available CPU time was lost due to load imbalance 68: in the domain decomposition. 68: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 68: You can also consider manually changing the decomposition (option -dd); 68: e.g. by using fewer domains along the box dimension in which there is 68: considerable inhomogeneity in the simulated system. 68: 68: 68: Dynamic load balancing report: 68: DLB was off during the run due to low measured imbalance. 68: Average load imbalance: 4.5%. 68: The balanceable part of the MD step is 21%, load imbalance is computed from this. 68: Part of the total run time spent waiting due to load imbalance: 0.9%. 68: 68: 68: NOTE: 13 % of the run time was spent in domain decomposition, 68: 5 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 29 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: 68: NOTE: 13 % of the run time was spent in domain decomposition, 68: 3 % of the run time was spent in pair search, 68: you might want to increase nstlist (this has no effect on accuracy) 68: 68: NOTE: 30 % of the run time was spent communicating energies, 68: you might want to increase some nst* mdp options 68: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 (11 ms) 68: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest (57 ms total) 68: 68: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 68: Setting the LD random seed to -2182307 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: Setting the LD random seed to -843229609 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: Setting the LD random seed to -408131 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 68: Setting the LD random seed to -1095240214 68: 68: Generated 3 of the 3 non-bonded parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -76580611 68: 68: Velocities were taken from a Maxwell distribution at 268 K 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 68: You have set rlist larger than the interaction cut-off, but you also have 68: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 68: 68: This is simulation 2 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 100 steps, 0.1 ps. 68: 68: Step 3: Run time exceeded 0.000 hours, will terminate the run within 400 steps 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 68: log). 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 68: 68: This is simulation 0 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 100 steps, 0.1 ps. 68: 68: Step 3: Run time exceeded 0.000 hours, will terminate the run within 400 steps 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -71435273 68: 68: Velocities were taken from a Maxwell distribution at 298 K 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to 1878785007 68: 68: Velocities were taken from a Maxwell distribution at 278 K 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Generated 3 of the 3 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: Setting gen_seed to -1186989057 68: 68: Velocities were taken from a Maxwell distribution at 288 K 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 68: 68: Calculated rlist for 1x1 atom pair-list as 0.726 nm, buffer size 0.026 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 68: 68: This is simulation 3 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 100 steps, 0.1 ps. 68: 68: Step 3: Run time exceeded 0.000 hours, will terminate the run within 400 steps 68: Number of degrees of freedom in T-Coupling group System is 9.00 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 notes 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Changing nstlist from 10 to 1, rlist from 0.726 to 0.7 68: 68: This is simulation 1 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 100 steps, 0.1 ps. 68: 68: Step 3: Run time exceeded 0.000 hours, will terminate the run within 400 steps 68: 68: Writing final coordinates. 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: 68: Writing final coordinates. 68: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 68: log). 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: 68: Writing final coordinates. 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: 68: Writing final coordinates. 68: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 68: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 68: Changing nstlist from 10 to 80, rlist from 0.726 to 0.974 68: 68: 68: This is simulation 2 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: 68: This is simulation 0 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 MPI process 68: 68: This is simulation 3 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: This is simulation 1 out of 4 running as a composite GROMACS 68: multi-simulation job. Setup for this simulation: 68: 68: Using 1 MPI process 68: Using 1 OpenMP thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'spc2' 68: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 68: starting mdrun 'spc2' 68: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 68: starting mdrun 'spc2' 68: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 68: starting mdrun 'spc2' 68: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: 68: Writing final coordinates. 68: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (27 ms) 68: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (27 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 5 tests from 2 test suites ran. (314 ms total) 68: [ PASSED ] 5 tests. 68/81 Test #68: MdrunMultiSimReplexTests ....................... Passed 0.79 sec test 69 Start 69: MdrunMultiSimReplexEquivalenceTests 69: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-multisim-replex-equivalence-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 10 tests from 2 test suites. 69: [----------] Global test environment set-up. 69: [----------] 8 tests from LF/ReplicaExchangeTest 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 278 K 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 288 K 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 298 K 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 268 K 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 69: log). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 3 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: This is simulation 2 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: This is simulation 1 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: This is simulation 0 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 trr version: GMX_trn_file (single precision) 69: 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s (717 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 278 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: 69: There was 1 warning 69: 69: This run will generate roughly 0 Mb of data 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 288 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: 69: There was 1 warning 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 298 K 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: There were 2 notes 69: 69: There was 1 warning 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 268 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: 69: There was 1 warning 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 2 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 3 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 1 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 69: log). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 0 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s (678 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 278 K 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 288 K 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 notes 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 notes 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 268 K 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 298 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: There were 3 notes 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 notes 69: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 69: log). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 2 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: This is simulation 3 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: This is simulation 1 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: This is simulation 0 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: Using 1 OpenMP thread 69: 69: Using 1 OpenMP thread 69: 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s (641 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 278 K 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 288 K 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 notes 69: 69: There was 1 warning 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 notes 69: 69: There was 1 warning 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 298 K 69: 69: Velocities were taken from a Maxwell distribution at 268 K 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 notes 69: 69: There was 1 warning 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 notes 69: 69: There was 1 warning 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 1 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 69: log). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 0 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 3 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 2 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s (662 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 278 K 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 298 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 69: log). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 1 out of 2 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 2 MPI processes 69: This is simulation 0 out of 2 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 2 MPI processes 69: Using 1 OpenMP thread per MPI process 69: 69: Using 1 OpenMP thread per MPI process 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: 69: Dynamic load balancing report: 69: DLB was off during the run due to low measured imbalance. 69: Average load imbalance: 3.5%. 69: The balanceable part of the MD step is 52%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 1.8%. 69: 69: 69: 69: Dynamic load balancing report: 69: DLB was off during the run due to low measured imbalance. 69: Average load imbalance: 2.1%. 69: The balanceable part of the MD step is 50%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 1.1%. 69: 69: 69: NOTE: 15 % of the run time was spent in domain decomposition, 69: 2 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: NOTE: 7 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: 69: NOTE: 13 % of the run time was spent in domain decomposition, 69: 3 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: NOTE: 6 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s (461 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 298 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: 69: There was 1 warning 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 278 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: 69: There was 1 warning 69: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 69: log). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 0 out of 2 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 2 MPI processes 69: Using 1 OpenMP thread per MPI process 69: 69: This is simulation 1 out of 2 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 2 MPI processes 69: Using 1 OpenMP thread per MPI process 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: 69: Dynamic load balancing report: 69: DLB was off during the run due to low measured imbalance. 69: Average load imbalance: 2.9%. 69: The balanceable part of the MD step is 54%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 1.6%. 69: 69: 69: 69: Dynamic load balancing report: 69: DLB was off during the run due to low measured imbalance. 69: Average load imbalance: 0.9%. 69: The balanceable part of the MD step is 57%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 0.5%. 69: 69: 69: NOTE: 14 % of the run time was spent in domain decomposition, 69: 2 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: NOTE: 6 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: 69: NOTE: 12 % of the run time was spent in domain decomposition, 69: 3 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: NOTE: 6 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s (472 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 298 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 notes 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 278 K 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 notes 69: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 69: log). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 0 out of 2 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 2 MPI processes 69: Using 1 OpenMP thread per MPI process 69: 69: This is simulation 1 out of 2 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 2 MPI processes 69: Using 1 OpenMP thread per MPI process 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: 69: Dynamic load balancing report: 69: DLB was turned on during the run due to measured imbalance. 69: Average load imbalance: 6.7%. 69: The balanceable part of the MD step is 47%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 3.2%. 69: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 69: 69: 69: NOTE: 13 % of the run time was spent in domain decomposition, 69: 3 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: NOTE: 7 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: 69: Writing final coordinates. 69: 69: 69: Dynamic load balancing report: 69: DLB was off during the run due to low measured imbalance. 69: Average load imbalance: 0.2%. 69: The balanceable part of the MD step is 39%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 0.1%. 69: 69: 69: NOTE: 10 % of the run time was spent in domain decomposition, 69: 2 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: NOTE: 5 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s (465 ms) 69: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are generating velocities so I am assuming you are equilibrating a 69: system. You are using Parrinello-Rahman pressure coupling, but this can 69: be unstable for equilibration. If your system crashes, try equilibrating 69: first with Berendsen pressure coupling. If you are not equilibrating the 69: system, you can probably ignore this warning. 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 298 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 notes 69: 69: There was 1 warning 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 278 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 notes 69: 69: There was 1 warning 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 69: log). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 0 out of 2 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 2 MPI processes 69: Using 1 OpenMP thread per MPI process 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: 69: Dynamic load balancing report: 69: DLB was off during the run due to low measured imbalance. 69: Average load imbalance: 2.5%. 69: The balanceable part of the MD step is 52%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 1.3%. 69: 69: 69: NOTE: 11 % of the run time was spent in domain decomposition, 69: 2 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: NOTE: 6 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 1 out of 2 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 2 MPI processes 69: Using 1 OpenMP thread per MPI process 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: 69: Dynamic load balancing report: 69: DLB was off during the run due to low measured imbalance. 69: Average load imbalance: 1.4%. 69: The balanceable part of the MD step is 57%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 0.8%. 69: 69: 69: NOTE: 12 % of the run time was spent in domain decomposition, 69: 2 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: NOTE: 6 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s (469 ms) 69: [----------] 8 tests from LF/ReplicaExchangeTest (4576 ms total) 69: 69: [----------] 2 tests from VV/ReplicaExchangeTest 69: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 278 K 69: 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: There were 2 notes 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 288 K 69: 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: There were 2 notes 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 298 K 69: 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: There were 2 notes 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 268 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: There were 2 notes 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 69: log). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 3 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 2 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 1 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 0 out of 4 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 1 MPI process 69: Using 1 OpenMP thread 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s (749 ms) 69: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 69: You have set rlist larger than the interaction cut-off, but you also have 69: verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance. 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 298 K 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Velocities were taken from a Maxwell distribution at 278 K 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.741 nm, buffer size 0.041 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 notes 69: This run will generate roughly 0 Mb of data 69: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 69: log). 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: Changing nstlist from 10 to 40, rlist from 0.735 to 0.879 69: 69: This is simulation 1 out of 2 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 2 MPI processes 69: Using 1 OpenMP thread per MPI process 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: This is simulation 0 out of 2 running as a composite GROMACS 69: multi-simulation job. Setup for this simulation: 69: 69: Using 2 MPI processes 69: Using 1 OpenMP thread per MPI process 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: 69: Writing final coordinates. 69: 69: Writing final coordinates. 69: 69: 69: Dynamic load balancing report: 69: DLB was off during the run due to low measured imbalance. 69: Average load imbalance: 3.2%. 69: The balanceable part of the MD step is 42%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 1.3%. 69: 69: 69: NOTE: 11 % of the run time was spent in domain decomposition, 69: 2 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: NOTE: 10 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: 69: 69: Dynamic load balancing report: 69: DLB was off during the run due to low measured imbalance. 69: Average load imbalance: 0.3%. 69: The balanceable part of the MD step is 41%, load imbalance is computed from this. 69: Part of the total run time spent waiting due to load imbalance: 0.1%. 69: 69: 69: NOTE: 11 % of the run time was spent in domain decomposition, 69: 2 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: NOTE: 11 % of the run time was spent communicating energies, 69: you might want to increase some nst* mdp options 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 69: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s (447 ms) 69: [----------] 2 tests from VV/ReplicaExchangeTest (1198 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 10 tests from 2 test suites ran. (5984 ms total) 69: [ PASSED ] 10 tests. 69/81 Test #69: MdrunMultiSimReplexEquivalenceTests ............ Passed 6.51 sec test 70 Start 70: MdrunMpi1RankPmeTests 70: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 19 tests from 1 test suite. 70: [----------] Global test environment set-up. 70: [----------] 19 tests from ReproducesEnergies/PmeTest 70: Setting the LD random seed to -16965 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: Number of degrees of freedom in T-Coupling group rest is 12.00 70: 70: The largest distance between excluded atoms is 0.190 nm 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: NVE simulation: will use the initial temperature of 1046.791 K for 70: determining the Verlet buffer size 70: 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 70: 70: Estimate for the relative computational load of the PME mesh part: 1.00 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: There were 2 notes 70: Setting the LD random seed to -538447877 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: For a correct single-point energy evaluation with nsteps = 0, use 70: continuation = yes to avoid constraining the input coordinates. 70: 70: 70: Generated 8 of the 10 non-bonded parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'Methanol' 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Searching the wall atom type(s) 70: Number of degrees of freedom in T-Coupling group rest is 13.00 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: NVE simulation: will use the initial temperature of 966.268 K for 70: determining the Verlet buffer size 70: 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 70: The optimal PME mesh load for parallel simulations is below 0.5 70: and for highly parallel simulations between 0.25 and 0.33, 70: for higher performance, increase the cut-off and the PME grid spacing. 70: 70: 70: 70: There were 3 notes 70: 70: The largest distance between excluded atoms is 0.190 nm 70: 70: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 70: 70: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 70: 70: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 70: 70: Note that mdrun will redetermine rlist based on the actual pair-list setup 70: Calculating fourier grid dimensions for X Y Z 70: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 70: 70: Estimate for the relative computational load of the PME mesh part: 1.00 70: 70: This run will generate roughly 0 Mb of data 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 70: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads 70: 70: starting mdrun 'spc-and-methanol' 70: 20 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.067 0.033 199.4 70: (ns/day) (hour/ns) 70: Performance: 54.212 0.443 70: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (213 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 70: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads 70: 70: starting mdrun 'spc-and-methanol' 70: 20 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.064 0.032 199.5 70: (ns/day) (hour/ns) 70: Performance: 56.368 0.426 70: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (42 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 70: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads 70: 70: starting mdrun 'spc-and-methanol' 70: 0 steps, 0.0 ps. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.010 0.005 195.4 70: (ns/day) (hour/ns) 70: Performance: 16.461 1.458 70: [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (649 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets using PME rank(s) but the simulation is using only one rank 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 70: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 70: log). 70: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 70: Can not increase nstlist because an NVE ensemble is used 70: Using 1 MPI process 70: 70: Non-default thread affinity set, disabling internal thread affinity 70: 70: Using 2 OpenMP threads 70: 70: starting mdrun 'spc-and-methanol' 70: 20 steps, 0.0 ps. 70: 70: Writing final coordinates. 70: 70: Core t (s) Wall t (s) (%) 70: Time: 0.065 0.033 199.3 70: (ns/day) (hour/ns) 70: Performance: 55.794 0.430 70: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (43 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 70: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 70: ./src/programs/mdrun/tests/pmetest.cpp:316: Skipped 70: Test is being skipped because: 70: it targets GPU execution, but no compatible devices were detected 70: PME GPU does not support: 70: Non-GPU build of GROMACS. 70: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 70: [----------] 19 tests from ReproducesEnergies/PmeTest (952 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 19 tests from 1 test suite ran. (1043 ms total) 70: [ PASSED ] 4 tests. 70: [ SKIPPED ] 15 tests, listed below: 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 70: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 70/81 Test #70: MdrunMpi1RankPmeTests .......................... Passed 1.59 sec test 71 Start 71: MdrunMpi2RankPmeTests 71: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 19 tests from 1 test suite. 71: [----------] Global test environment set-up. 71: [----------] 19 tests from ReproducesEnergies/PmeTest 71: Setting the LD random seed to -537444353 71: 71: Generated 8 of the 10 non-bonded parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'Methanol' 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: Number of degrees of freedom in T-Coupling group rest is 12.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: NVE simulation: will use the initial temperature of 1046.791 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 notes 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: 71: The largest distance between excluded atoms is 0.190 nm 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to -2056421379 71: 71: Generated 8 of the 10 non-bonded parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'Methanol' 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Searching the wall atom type(s) 71: Number of degrees of freedom in T-Coupling group rest is 13.00 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: NVE simulation: will use the initial temperature of 966.268 K for 71: determining the Verlet buffer size 71: 71: 71: The largest distance between excluded atoms is 0.190 nm 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 3 notes 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI processes 71: 71: Non-default thread affinity set, disabling internal thread affinity 71: 71: Using 2 OpenMP threads per MPI process 71: 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was off during the run due to low measured imbalance. 71: Average load imbalance: 7.1%. 71: The balanceable part of the MD step is 19%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 1.3%. 71: 71: 71: NOTE: 6 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.123 0.031 398.4 71: (ns/day) (hour/ns) 71: Performance: 58.652 0.409 71: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (205 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 71: Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI processes 71: 71: Non-default thread affinity set, disabling internal thread affinity 71: 71: Using 2 OpenMP threads per MPI process 71: 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was off during the run due to low measured imbalance. 71: Average load imbalance: 7.2%. 71: The balanceable part of the MD step is 14%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 1.0%. 71: 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.147 0.037 398.9 71: (ns/day) (hour/ns) 71: Performance: 49.130 0.489 71: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (48 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI processes 71: 71: Non-default thread affinity set, disabling internal thread affinity 71: 71: Using 2 OpenMP threads per MPI process 71: 71: starting mdrun 'spc-and-methanol' 71: 0 steps, 0.0 ps. 71: [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (622 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.018 0.005 385.5 71: (ns/day) (hour/ns) 71: Performance: 18.856 1.273 71: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI processes 71: 71: Non-default thread affinity set, disabling internal thread affinity 71: 71: Using 2 OpenMP threads per MPI process 71: 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.302 0.076 399.3 71: (ns/day) (hour/ns) 71: Performance: 24.015 0.999 71: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (127 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI processes 71: 71: Non-default thread affinity set, disabling internal thread affinity 71: 71: Using 2 OpenMP threads per MPI process 71: 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.124 0.031 398.6 71: (ns/day) (hour/ns) 71: Performance: 58.393 0.411 71: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_auto.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (38 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI processes 71: 71: Non-default thread affinity set, disabling internal thread affinity 71: 71: Using 2 OpenMP threads per MPI process 71: 71: starting mdrun 'spc-and-methanol' 71: 0 steps, 0.0 ps. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 1.284 0.321 399.8 71: (ns/day) (hour/ns) 71: Performance: 0.269 89.214 71: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (642 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 71: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 71: log). 71: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI processes 71: 71: Non-default thread affinity set, disabling internal thread affinity 71: 71: Using 2 OpenMP threads per MPI process 71: 71: starting mdrun 'spc-and-methanol' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was off during the run due to low measured imbalance. 71: Average load imbalance: 7.1%. 71: The balanceable part of the MD step is 19%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 1.3%. 71: 71: 71: NOTE: 7 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.123 0.031 398.4 71: (ns/day) (hour/ns) 71: Performance: 58.774 0.408 71: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (42 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 71: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 71: [----------] 19 tests from ReproducesEnergies/PmeTest (1730 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 19 tests from 1 test suite ran. (1814 ms total) 71: [ PASSED ] 7 tests. 71: [ SKIPPED ] 12 tests, listed below: 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 71: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 71/81 Test #71: MdrunMpi2RankPmeTests .......................... Passed 2.98 sec test 72 Start 72: MdrunMpiCoordinationBasicTestsOneRank 72: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-mpi-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMpiCoordinationBasicTestsOneRank.xml" 72: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 72: Test timeout computed to be: 1920 72: [==========] Running 1 test from 1 test suite. 72: [----------] Global test environment set-up. 72: [----------] 1 test from BasicPropagators/PeriodicActionsTest 72: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (1) 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI process 72: 72: Non-default thread affinity set, disabling internal thread affinity 72: 72: Using 1 OpenMP thread 72: 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.004 0.004 98.3 72: (ns/day) (hour/ns) 72: Performance: 349.795 0.069 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (1) 72: 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: There were 3 notes 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI process 72: 72: Non-default thread affinity set, disabling internal thread affinity 72: 72: Using 1 OpenMP thread 72: 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 94.9 72: (ns/day) (hour/ns) 72: Performance: 767.197 0.031 72: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: Setting nstcalcenergy (100) equal to nstenergy (4) 72: 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 5 notes 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI process 72: 72: Non-default thread affinity set, disabling internal thread affinity 72: 72: Using 1 OpenMP thread 72: 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 95.1 72: (ns/day) (hour/ns) 72: Performance: 741.436 0.032 72: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 72: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 4 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI process 72: 72: Non-default thread affinity set, disabling internal thread affinity 72: 72: Using 1 OpenMP thread 72: 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 96.3 72: (ns/day) (hour/ns) 72: Performance: 668.903 0.036 72: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 4 notes 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI process 72: 72: Non-default thread affinity set, disabling internal thread affinity 72: 72: Using 1 OpenMP thread 72: 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 95.4 72: (ns/day) (hour/ns) 72: Performance: 812.850 0.030 72: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 72: 72: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 72: that with the Verlet scheme, nstlist has no effect on the accuracy of 72: your simulation. 72: 72: 72: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 72: setting nstcomm equal to nstcalcenergy for less overhead 72: 72: Generated 1 of the 1 non-bonded parameter combinations 72: 72: Excluding 1 bonded neighbours molecule type 'Argon' 72: Number of degrees of freedom in T-Coupling group System is 33.00 72: 72: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: NVE simulation: will use the initial temperature of 68.810 K for 72: determining the Verlet buffer size 72: 72: 72: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 72: 72: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 72: 72: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 72: 72: Note that mdrun will redetermine rlist based on the actual pair-list setup 72: 72: This run will generate roughly 0 Mb of data 72: 72: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 72: COM removal frequency is set to (1). 72: Other settings require a global communication frequency of 4. 72: Note that this will require additional global communication steps, 72: which will reduce performance when using multiple ranks. 72: Consider setting nstcomm to a multiple of 4. 72: 72: 72: There were 4 notes 72: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 72: log). 72: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 72: Can not increase nstlist because an NVE ensemble is used 72: Using 1 MPI process 72: 72: Non-default thread affinity set, disabling internal thread affinity 72: 72: Using 1 OpenMP thread 72: 72: starting mdrun 'Argon' 72: 16 steps, 0.0 ps. 72: 72: Writing final coordinates. 72: 72: Core t (s) Wall t (s) (%) 72: Time: 0.002 0.002 96.2 72: (ns/day) (hour/ns) 72: Performance: 876.329 0.027 72: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 72: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 72: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (63 ms) 72: [----------] 1 test from BasicPropagators/PeriodicActionsTest (63 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 1 test from 1 test suite ran. (150 ms total) 72: [ PASSED ] 1 test. 72/81 Test #72: MdrunMpiCoordinationBasicTestsOneRank .......... Passed 0.62 sec test 73 Start 73: MdrunMpiCoordinationBasicTestsTwoRanks 73: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-mpi-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMpiCoordinationBasicTestsTwoRanks.xml" 73: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 73: Test timeout computed to be: 1920 73: [==========] Running 1 test from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 1 test from BasicPropagators/PeriodicActionsTest 73: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: Setting nstcalcenergy (100) equal to nstenergy (1) 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: There were 3 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 1 OpenMP thread per MPI process 73: 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 1.5%. 73: The balanceable part of the MD step is 64%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 0.9%. 73: 73: 73: NOTE: 35 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.009 0.005 194.0 73: (ns/day) (hour/ns) 73: Performance: 312.427 0.077 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: Setting nstcalcenergy (100) equal to nstenergy (1) 73: 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: There were 3 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 1 OpenMP thread per MPI process 73: 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was turned on during the run due to measured imbalance. 73: Average load imbalance: 4.0%. 73: The balanceable part of the MD step is 58%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 2.4%. 73: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 73: 73: 73: NOTE: 32 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.005 0.003 193.1 73: (ns/day) (hour/ns) 73: Performance: 519.618 0.046 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 10 time 0.010 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 15 time 0.015 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 14 time 0.014 Reading energy frame 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: Setting nstcalcenergy (100) equal to nstenergy (4) 73: 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 5 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 1 OpenMP thread per MPI process 73: 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 1.5%. 73: The balanceable part of the MD step is 63%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 1.0%. 73: 73: 73: NOTE: 33 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.004 0.002 192.3 73: (ns/day) (hour/ns) 73: Performance: 642.900 0.037 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 1 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 5 time 0.005 Reading energy frame 4 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 8 time 0.008 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.012 Last energy frame read 4 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 4 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 1 OpenMP thread per MPI process 73: 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 1.7%. 73: The balanceable part of the MD step is 60%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 1.0%. 73: 73: 73: NOTE: 34 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.004 0.002 191.9 73: (ns/day) (hour/ns) 73: Performance: 656.220 0.037 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 4 notes 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 1 OpenMP thread per MPI process 73: 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 1.7%. 73: The balanceable part of the MD step is 63%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 1.1%. 73: 73: 73: NOTE: 34 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.005 0.002 193.3 73: (ns/day) (hour/ns) 73: Performance: 589.954 0.041 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 73: that with the Verlet scheme, nstlist has no effect on the accuracy of 73: your simulation. 73: 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 73: setting nstcomm equal to nstcalcenergy for less overhead 73: 73: Generated 1 of the 1 non-bonded parameter combinations 73: 73: Excluding 1 bonded neighbours molecule type 'Argon' 73: Number of degrees of freedom in T-Coupling group System is 33.00 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: NVE simulation: will use the initial temperature of 68.810 K for 73: determining the Verlet buffer size 73: 73: 73: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 73: 73: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: 73: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 73: COM removal frequency is set to (1). 73: Other settings require a global communication frequency of 4. 73: Note that this will require additional global communication steps, 73: which will reduce performance when using multiple ranks. 73: Consider setting nstcomm to a multiple of 4. 73: 73: 73: There were 4 notes 73: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 73: log). 73: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: 73: Non-default thread affinity set, disabling internal thread affinity 73: 73: Using 1 OpenMP thread per MPI process 73: 73: starting mdrun 'Argon' 73: 16 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 1.6%. 73: The balanceable part of the MD step is 59%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 1.0%. 73: 73: 73: NOTE: 34 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.005 0.002 193.0 73: (ns/day) (hour/ns) 73: Performance: 612.415 0.039 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 73: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 73: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (69 ms) 73: [----------] 1 test from BasicPropagators/PeriodicActionsTest (69 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (158 ms total) 73: [ PASSED ] 1 test. 73/81 Test #73: MdrunMpiCoordinationBasicTestsTwoRanks ......... Passed 0.68 sec test 74 Start 74: MdrunMpiCoordinationCouplingTestsOneRank 74: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-mpi-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMpiCoordinationCouplingTestsOneRank.xml" 74: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 74: Test timeout computed to be: 1920 74: [==========] Running 22 tests from 1 test suite. 74: [----------] Global test environment set-up. 74: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.005 98.4 74: (ns/day) (hour/ns) 74: Performance: 304.152 0.079 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 824.822 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.002 94.3 74: (ns/day) (hour/ns) 74: Performance: 975.704 0.025 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 883.239 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.5 74: (ns/day) (hour/ns) 74: Performance: 813.709 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.3 74: (ns/day) (hour/ns) 74: Performance: 857.544 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (68 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 96.3 74: (ns/day) (hour/ns) 74: Performance: 387.654 0.062 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 94.5 74: (ns/day) (hour/ns) 74: Performance: 474.695 0.051 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.5 74: (ns/day) (hour/ns) 74: Performance: 722.990 0.033 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: There were 3 notes 74: 74: There was 1 warning 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 93.7 74: (ns/day) (hour/ns) 74: Performance: 754.235 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.018 0.018 99.1 74: (ns/day) (hour/ns) 74: Performance: 81.929 0.293 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.055 0.055 99.9 74: (ns/day) (hour/ns) 74: Performance: 26.699 0.899 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (419 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.0 74: (ns/day) (hour/ns) 74: Performance: 823.389 0.029 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 96.2 74: (ns/day) (hour/ns) 74: Performance: 1053.273 0.023 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 95.7 74: (ns/day) (hour/ns) 74: Performance: 1097.754 0.022 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 94.6 74: (ns/day) (hour/ns) 74: Performance: 990.290 0.024 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.002 95.0 74: (ns/day) (hour/ns) 74: Performance: 968.799 0.025 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.174 0.174 99.9 74: (ns/day) (hour/ns) 74: Performance: 8.429 2.847 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (221 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 657.761 0.036 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.003 92.3 74: (ns/day) (hour/ns) 74: Performance: 584.219 0.041 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 95.0 74: (ns/day) (hour/ns) 74: Performance: 1007.786 0.024 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.4 74: (ns/day) (hour/ns) 74: Performance: 804.886 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.3 74: (ns/day) (hour/ns) 74: Performance: 883.493 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 973.391 0.025 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (62 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.3 74: (ns/day) (hour/ns) 74: Performance: 637.215 0.038 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.9 74: (ns/day) (hour/ns) 74: Performance: 690.108 0.035 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.0 74: (ns/day) (hour/ns) 74: Performance: 856.709 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.6 74: (ns/day) (hour/ns) 74: Performance: 766.529 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.6 74: (ns/day) (hour/ns) 74: Performance: 718.269 0.033 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.8 74: (ns/day) (hour/ns) 74: Performance: 781.206 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (74 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 610.262 0.039 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 904.374 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 733.491 0.033 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 778.147 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.9 74: (ns/day) (hour/ns) 74: Performance: 754.235 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.8 74: (ns/day) (hour/ns) 74: Performance: 759.255 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (63 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.0 74: (ns/day) (hour/ns) 74: Performance: 539.835 0.044 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: 74: There were 2 notes 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.5 74: (ns/day) (hour/ns) 74: Performance: 649.304 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.005 96.3 74: (ns/day) (hour/ns) 74: Performance: 288.013 0.083 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.4 74: (ns/day) (hour/ns) 74: Performance: 791.545 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.3 74: (ns/day) (hour/ns) 74: Performance: 807.206 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 774.625 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (69 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 96.7 74: (ns/day) (hour/ns) 74: Performance: 532.095 0.045 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 940.262 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.8 74: (ns/day) (hour/ns) 74: Performance: 819.773 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 857.902 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.3 74: (ns/day) (hour/ns) 74: Performance: 836.810 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 705.035 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (73 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.3 74: (ns/day) (hour/ns) 74: Performance: 658.394 0.036 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 798.522 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.6 74: (ns/day) (hour/ns) 74: Performance: 838.518 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 94.9 74: (ns/day) (hour/ns) 74: Performance: 864.645 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.4 74: (ns/day) (hour/ns) 74: Performance: 817.706 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: There was 1 warning 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.6 74: (ns/day) (hour/ns) 74: Performance: 891.032 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (61 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.9 74: (ns/day) (hour/ns) 74: Performance: 698.480 0.034 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 758.134 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.4 74: (ns/day) (hour/ns) 74: Performance: 927.800 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.2 74: (ns/day) (hour/ns) 74: Performance: 749.920 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.7 74: (ns/day) (hour/ns) 74: Performance: 737.178 0.033 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (64 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 97.5 74: (ns/day) (hour/ns) 74: Performance: 369.252 0.065 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: There were 3 notes 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.1 74: (ns/day) (hour/ns) 74: Performance: 556.412 0.043 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.005 0.005 97.7 74: (ns/day) (hour/ns) 74: Performance: 299.000 0.080 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: There were 3 notes 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.8 74: (ns/day) (hour/ns) 74: Performance: 788.203 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: There were 3 notes 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 95.1 74: (ns/day) (hour/ns) 74: Performance: 772.198 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.006 98.3 74: (ns/day) (hour/ns) 74: Performance: 255.987 0.094 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 74: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.0 74: (ns/day) (hour/ns) 74: Performance: 722.142 0.033 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (70 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 97.9 74: (ns/day) (hour/ns) 74: Performance: 351.251 0.068 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: There were 2 notes 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.9 74: (ns/day) (hour/ns) 74: Performance: 862.466 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 96.1 74: (ns/day) (hour/ns) 74: Performance: 1023.695 0.023 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 97.9 74: (ns/day) (hour/ns) 74: Performance: 398.718 0.060 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 846.352 0.028 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.7 74: (ns/day) (hour/ns) 74: Performance: 928.919 0.026 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (62 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.9 74: (ns/day) (hour/ns) 74: Performance: 597.072 0.040 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.9 74: (ns/day) (hour/ns) 74: Performance: 879.206 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: There were 2 notes 74: 74: There was 1 warning 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 96.6 74: (ns/day) (hour/ns) 74: Performance: 1024.546 0.023 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.001 0.001 96.5 74: (ns/day) (hour/ns) 74: Performance: 985.380 0.024 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 830.045 0.029 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.8 74: (ns/day) (hour/ns) 74: Performance: 786.794 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (64 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.1 74: (ns/day) (hour/ns) 74: Performance: 626.204 0.038 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 684.054 0.035 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 901.990 0.027 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.007 0.007 98.9 74: (ns/day) (hour/ns) 74: Performance: 197.480 0.122 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.2 74: (ns/day) (hour/ns) 74: Performance: 792.563 0.030 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 741.347 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (74 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.4 74: (ns/day) (hour/ns) 74: Performance: 612.142 0.039 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.0 74: (ns/day) (hour/ns) 74: Performance: 639.265 0.038 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.7 74: (ns/day) (hour/ns) 74: Performance: 707.058 0.034 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.1 74: (ns/day) (hour/ns) 74: Performance: 679.827 0.035 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.8 74: (ns/day) (hour/ns) 74: Performance: 630.433 0.038 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 4. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 4. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.0 74: (ns/day) (hour/ns) 74: Performance: 689.953 0.035 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (64 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.0 74: (ns/day) (hour/ns) 74: Performance: 330.504 0.073 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.9 74: (ns/day) (hour/ns) 74: Performance: 678.554 0.035 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.8 74: (ns/day) (hour/ns) 74: Performance: 678.629 0.035 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 98.1 74: (ns/day) (hour/ns) 74: Performance: 728.117 0.033 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.9 74: (ns/day) (hour/ns) 74: Performance: 610.867 0.039 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 74: NVE simulation: will use the initial temperature of 68.810 K for 74: determining the Verlet buffer size 74: 74: 74: There were 3 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Can not increase nstlist because an NVE ensemble is used 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.006 98.8 74: (ns/day) (hour/ns) 74: Performance: 234.003 0.103 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (75 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.009 0.009 99.1 74: (ns/day) (hour/ns) 74: Performance: 157.471 0.152 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.8 74: (ns/day) (hour/ns) 74: Performance: 743.674 0.032 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.1 74: (ns/day) (hour/ns) 74: Performance: 769.689 0.031 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.003 97.1 74: (ns/day) (hour/ns) 74: Performance: 579.821 0.041 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.015 0.015 99.3 74: (ns/day) (hour/ns) 74: Performance: 96.605 0.248 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.5 74: (ns/day) (hour/ns) 74: Performance: 682.085 0.035 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (120 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.9 74: (ns/day) (hour/ns) 74: Performance: 544.896 0.044 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 96.7 74: (ns/day) (hour/ns) 74: Performance: 624.300 0.038 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.0 74: (ns/day) (hour/ns) 74: Performance: 662.358 0.036 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.108 0.108 99.9 74: (ns/day) (hour/ns) 74: Performance: 13.617 1.763 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.3 74: (ns/day) (hour/ns) 74: Performance: 663.500 0.036 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 74: The Berendsen barostat does not generate any strictly correct ensemble, 74: and should not be used for new production simulations (in our opinion). 74: For isotropic scaling we would recommend the C-rescale barostat that also 74: ensures fast relaxation without oscillations, and for anisotropic scaling 74: you likely want to use the Parrinello-Rahman barostat. 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: There was 1 warning 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.007 0.007 98.9 74: (ns/day) (hour/ns) 74: Performance: 201.392 0.119 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (200 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.006 0.007 98.1 74: (ns/day) (hour/ns) 74: Performance: 222.019 0.108 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.3 74: (ns/day) (hour/ns) 74: Performance: 631.985 0.038 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.0 74: (ns/day) (hour/ns) 74: Performance: 467.101 0.051 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.5 74: (ns/day) (hour/ns) 74: Performance: 658.042 0.036 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.003 97.7 74: (ns/day) (hour/ns) 74: Performance: 583.169 0.041 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (129 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.2 74: (ns/day) (hour/ns) 74: Performance: 655.801 0.037 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.0 74: (ns/day) (hour/ns) 74: Performance: 510.575 0.047 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.7 74: (ns/day) (hour/ns) 74: Performance: 529.898 0.045 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: 74: This run will generate roughly 0 Mb of data 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.2 74: (ns/day) (hour/ns) 74: Performance: 570.637 0.042 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.7 74: (ns/day) (hour/ns) 74: Performance: 550.200 0.044 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.9 74: (ns/day) (hour/ns) 74: Performance: 514.584 0.047 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.003 97.7 74: (ns/day) (hour/ns) 74: Performance: 587.507 0.041 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (130 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.004 0.004 98.0 74: (ns/day) (hour/ns) 74: Performance: 332.538 0.072 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: There were 3 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.7 74: (ns/day) (hour/ns) 74: Performance: 422.943 0.057 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.004 97.7 74: (ns/day) (hour/ns) 74: Performance: 416.425 0.058 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.004 97.5 74: (ns/day) (hour/ns) 74: Performance: 416.144 0.058 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.004 97.9 74: (ns/day) (hour/ns) 74: Performance: 417.809 0.057 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: for current Trotter decomposition methods with vv, nsttcouple and 74: nstpcouple must be equal. Both have been reset to 74: min(nsttcouple,nstpcouple) = 2 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 74: COM removal frequency is set to (5). 74: Other settings require a global communication frequency of 2. 74: Note that this will require additional global communication steps, 74: which will reduce performance when using multiple ranks. 74: Consider setting nstcomm to a multiple of 2. 74: 74: 74: There were 4 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 98.1 74: (ns/day) (hour/ns) 74: Performance: 530.263 0.045 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (119 ms) 74: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.4 74: (ns/day) (hour/ns) 74: Performance: 457.628 0.052 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (1) 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 95.4 74: (ns/day) (hour/ns) 74: Performance: 537.011 0.045 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: Setting nstcalcenergy (100) equal to nstenergy (4) 74: 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.002 0.002 97.3 74: (ns/day) (hour/ns) 74: Performance: 624.933 0.038 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 74: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.9 74: (ns/day) (hour/ns) 74: Performance: 537.949 0.045 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.2 74: (ns/day) (hour/ns) 74: Performance: 460.330 0.052 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 74: Generated 1 of the 1 non-bonded parameter combinations 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 74: that with the Verlet scheme, nstlist has no effect on the accuracy of 74: your simulation. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 74: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 74: setting nstcomm equal to nstcalcenergy for less overhead 74: 74: 74: Excluding 1 bonded neighbours molecule type 'Argon' 74: Number of degrees of freedom in T-Coupling group System is 33.00 74: 74: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 notes 74: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 74: log). 74: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 74: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 74: 74: Using 1 MPI process 74: 74: Non-default thread affinity set, disabling internal thread affinity 74: 74: Using 1 OpenMP thread 74: 74: starting mdrun 'Argon' 74: 16 steps, 0.0 ps. 74: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (345 ms) 74: 74: Writing final coordinates. 74: 74: Core t (s) Wall t (s) (%) 74: Time: 0.003 0.003 97.6 74: (ns/day) (hour/ns) 74: Performance: 465.477 0.052 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 74: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 74: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (2637 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 22 tests from 1 test suite ran. (2729 ms total) 74: [ PASSED ] 22 tests. 74/81 Test #74: MdrunMpiCoordinationCouplingTestsOneRank ....... Passed 3.23 sec test 75 Start 75: MdrunMpiCoordinationCouplingTestsTwoRanks 75: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-mpi-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMpiCoordinationCouplingTestsTwoRanks.xml" 75: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 75: Test timeout computed to be: 1920 75: [==========] Running 22 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 6.1%. 75: The balanceable part of the MD step is 62%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 3.8%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 37 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.005 193.2 75: (ns/day) (hour/ns) 75: Performance: 317.810 0.076 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 4.9%. 75: The balanceable part of the MD step is 59%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.9%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.7 75: (ns/day) (hour/ns) 75: Performance: 674.505 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 9 time 0.009 Reading energy frame 11 time 0.011 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 10 time 0.010 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 12 time 0.012 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 15 time 0.015 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.3%. 75: The balanceable part of the MD step is 56%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.3%. 75: 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.6 75: (ns/day) (hour/ns) 75: Performance: 778.590 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.5%. 75: The balanceable part of the MD step is 54%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.3%. 75: 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.1 75: (ns/day) (hour/ns) 75: Performance: 723.626 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.4%. 75: The balanceable part of the MD step is 52%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.2%. 75: 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.8 75: (ns/day) (hour/ns) 75: Performance: 703.264 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 9.4%. 75: The balanceable part of the MD step is 52%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 4.9%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.5 75: (ns/day) (hour/ns) 75: Performance: 689.953 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (71 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.2%. 75: The balanceable part of the MD step is 60%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.7%. 75: 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 187.7 75: (ns/day) (hour/ns) 75: Performance: 539.150 0.045 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 4.1%. 75: The balanceable part of the MD step is 55%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.3%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.7 75: (ns/day) (hour/ns) 75: Performance: 649.030 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 5 time 0.005 Reading energy frame 2 time 0.002 Reading energy frame 5 time 0.005 Reading energy frame 3 time 0.003 Reading energy frame 6 time 0.006 Reading energy frame 3 time 0.003 Reading energy frame 6 time 0.006 Reading energy frame 4 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.004 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 7 time 0.007 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 10 time 0.010 Reading energy frame 14 time 0.014 Reading energy frame 11 time 0.011 Reading energy frame 14 time 0.014 Reading energy frame 11 time 0.011 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 16 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 3.1%. 75: The balanceable part of the MD step is 56%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.8%. 75: 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.4 75: (ns/day) (hour/ns) 75: Performance: 737.707 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 7.0%. 75: The balanceable part of the MD step is 53%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 3.7%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.3 75: (ns/day) (hour/ns) 75: Performance: 679.640 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.4%. 75: The balanceable part of the MD step is 57%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.4%. 75: 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.7 75: (ns/day) (hour/ns) 75: Performance: 637.413 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: 75: There was 1 warning 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.5%. 75: The balanceable part of the MD step is 65%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.0%. 75: 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.5 75: (ns/day) (hour/ns) 75: Performance: 656.045 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (62 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.7%. 75: The balanceable part of the MD step is 61%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.4%. 75: 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 191.3 75: (ns/day) (hour/ns) 75: Performance: 542.377 0.044 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.3%. 75: The balanceable part of the MD step is 61%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.8%. 75: 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 658.711 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 7.5%. 75: The balanceable part of the MD step is 55%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 4.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.5 75: (ns/day) (hour/ns) 75: Performance: 699.154 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 1 time 0.004 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 1 time 0.001 Reading energy frame 8 time 0.008 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 4 time 0.004 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 12 time 0.012 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 16 time 0.016 Reading energy frame 10 time 0.010 Last energy frame read 4 time 0.016 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.6%. 75: The balanceable part of the MD step is 57%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.9%. 75: 75: 75: NOTE: 43 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.010 0.005 195.2 75: (ns/day) (hour/ns) 75: Performance: 289.481 0.083 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 8.9%. 75: The balanceable part of the MD step is 57%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 5.1%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: NOTE: 5.1 % of the available CPU time was lost due to load imbalance 75: in the domain decomposition. 75: You can consider manually changing the decomposition (option -dd); 75: e.g. by using fewer domains along the box dimension in which there is 75: considerable inhomogeneity in the simulated system. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.3 75: (ns/day) (hour/ns) 75: Performance: 657.130 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 7.1%. 75: The balanceable part of the MD step is 56%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 3.9%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.0 75: (ns/day) (hour/ns) 75: Performance: 685.234 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (66 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 193.1 75: (ns/day) (hour/ns) 75: Performance: 609.025 0.039 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.6 75: (ns/day) (hour/ns) 75: Performance: 717.349 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 9 time 0.009 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 10 time 0.010 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 15 time 0.015 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 191.6 75: (ns/day) (hour/ns) 75: Performance: 807.629 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 35 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.8 75: (ns/day) (hour/ns) 75: Performance: 782.049 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.2 75: (ns/day) (hour/ns) 75: Performance: 789.769 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: 75: NOTE: 35 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 187.1 75: (ns/day) (hour/ns) 75: Performance: 751.155 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (81 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 192.4 75: (ns/day) (hour/ns) 75: Performance: 536.007 0.045 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 24 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 192.8 75: (ns/day) (hour/ns) 75: Performance: 533.986 0.045 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 3 time 0.003 Reading energy frame 6 time 0.006 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 11 time 0.011 Reading energy frame 14 time 0.014 Reading energy frame 11 time 0.011 Reading energy frame 14 time 0.014 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Last energy frame read 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.9 75: (ns/day) (hour/ns) 75: Performance: 727.128 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 35 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 193.2 75: (ns/day) (hour/ns) 75: Performance: 677.621 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.7 75: (ns/day) (hour/ns) 75: Performance: 797.849 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 44 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.004 194.0 75: (ns/day) (hour/ns) 75: Performance: 386.063 0.062 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (70 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 25 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 193.3 75: (ns/day) (hour/ns) 75: Performance: 564.855 0.042 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.9 75: (ns/day) (hour/ns) 75: Performance: 666.659 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Last energy frame read 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 188.9 75: (ns/day) (hour/ns) 75: Performance: 825.153 0.029 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.004 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.008 Reading energy frame 1 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 1 time 0.001 Reading energy frame 6 time 0.006 Reading energy frame 2 time 0.002 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 3 time 0.012 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 9 time 0.009 Reading energy frame 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Last energy frame read 4 time 0.016 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 37 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.0 75: (ns/day) (hour/ns) 75: Performance: 737.310 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: NOTE: 37 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.6 75: (ns/day) (hour/ns) 75: Performance: 796.920 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 36 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.7 75: (ns/day) (hour/ns) 75: Performance: 768.345 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (99 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 191.2 75: (ns/day) (hour/ns) 75: Performance: 529.556 0.045 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.1 75: (ns/day) (hour/ns) 75: Performance: 700.306 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 190.8 75: (ns/day) (hour/ns) 75: Performance: 834.034 0.029 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 36 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 188.9 75: (ns/day) (hour/ns) 75: Performance: 731.011 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 36 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.2 75: (ns/day) (hour/ns) 75: Performance: 713.858 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.0 75: (ns/day) (hour/ns) 75: Performance: 747.237 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (77 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.7 75: (ns/day) (hour/ns) 75: Performance: 669.703 0.036 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 185.9 75: (ns/day) (hour/ns) 75: Performance: 774.138 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 190.6 75: (ns/day) (hour/ns) 75: Performance: 906.036 0.026 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 2 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 5 time 0.005 Reading energy frame 4 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 8 time 0.008 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Last energy frame read 4 time 0.016 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 47 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.017 0.009 197.8 75: (ns/day) (hour/ns) 75: Performance: 167.530 0.143 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.7 75: (ns/day) (hour/ns) 75: Performance: 760.332 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 35 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 836.753 0.029 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (91 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 192.6 75: (ns/day) (hour/ns) 75: Performance: 565.322 0.042 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.2 75: (ns/day) (hour/ns) 75: Performance: 786.542 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 15 time 0.015 Reading energy frame 12 time 0.012 Reading energy frame 15 time 0.015 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Last energy frame read 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 187.3 75: (ns/day) (hour/ns) 75: Performance: 795.531 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 0 time 0.000 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 0 time 0.000 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Last energy frame read 4 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 36 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.5 75: (ns/day) (hour/ns) 75: Performance: 736.517 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 35 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.0 75: (ns/day) (hour/ns) 75: Performance: 758.694 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 35 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.0 75: (ns/day) (hour/ns) 75: Performance: 788.909 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (95 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 192.7 75: (ns/day) (hour/ns) 75: Performance: 535.634 0.045 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.2 75: (ns/day) (hour/ns) 75: Performance: 727.128 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 12 time 0.012 Reading energy frame 14 time 0.014 Reading energy frame 12 time 0.012 Reading energy frame 14 time 0.014 Reading energy frame 13 time 0.013 Reading energy frame 15 time 0.015 Reading energy frame 13 time 0.013 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: 75: NOTE: 36 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.3 75: (ns/day) (hour/ns) 75: Performance: 715.724 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 0 time 0.000 Reading energy frame 6 time 0.006 Reading energy frame 1 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 1 time 0.001 Reading energy frame 3 time 0.012 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 4 time 0.004 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 4 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 8 time 0.008 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.012 Last energy frame read 4 time 0.016 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.6 75: (ns/day) (hour/ns) 75: Performance: 699.551 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 35 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 189.8 75: (ns/day) (hour/ns) 75: Performance: 754.975 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: 75: There were 3 notes 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 36 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.2 75: (ns/day) (hour/ns) 75: Performance: 715.807 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (105 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 192.9 75: (ns/day) (hour/ns) 75: Performance: 618.037 0.039 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.1 75: (ns/day) (hour/ns) 75: Performance: 694.230 0.035 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 40 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 190.0 75: (ns/day) (hour/ns) 75: Performance: 574.495 0.042 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 36 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 743.405 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 33 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 191.2 75: (ns/day) (hour/ns) 75: Performance: 621.372 0.039 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 75: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 10 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.015 0.008 196.7 75: (ns/day) (hour/ns) 75: Performance: 193.422 0.124 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (262 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 30 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 193.0 75: (ns/day) (hour/ns) 75: Performance: 609.146 0.039 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 31 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.2 75: (ns/day) (hour/ns) 75: Performance: 777.166 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.1 75: (ns/day) (hour/ns) 75: Performance: 805.886 0.030 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: 75: This run will generate roughly 0 Mb of data 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 762.120 0.031 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 36 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.8 75: (ns/day) (hour/ns) 75: Performance: 669.666 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 35 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 193.0 75: (ns/day) (hour/ns) 75: Performance: 715.682 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (70 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.002 193.6 75: (ns/day) (hour/ns) 75: Performance: 590.350 0.041 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.199 0.100 199.8 75: (ns/day) (hour/ns) 75: Performance: 14.729 1.629 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 181.3 75: (ns/day) (hour/ns) 75: Performance: 708.848 0.034 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 37 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.6 75: (ns/day) (hour/ns) 75: Performance: 731.662 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: NOTE: 32 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 192.2 75: (ns/day) (hour/ns) 75: Performance: 650.332 0.037 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 1 % of the run time was spent in domain decomposition, 75: 27 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: NOTE: 17 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.005 196.4 75: (ns/day) (hour/ns) 75: Performance: 325.673 0.074 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (175 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 28 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 192.3 75: (ns/day) (hour/ns) 75: Performance: 555.284 0.043 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 41 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.004 195.5 75: (ns/day) (hour/ns) 75: Performance: 341.014 0.070 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 75: Writing final coordinates. 75: 75: NOTE: 34 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.003 0.002 190.5 75: (ns/day) (hour/ns) 75: Performance: 836.980 0.029 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: 75: NOTE: 37 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 190.9 75: (ns/day) (hour/ns) 75: Performance: 742.598 0.032 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 37 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.2 75: (ns/day) (hour/ns) 75: Performance: 725.416 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 37 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 191.9 75: (ns/day) (hour/ns) 75: Performance: 723.244 0.033 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (89 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 2.8%. 75: The balanceable part of the MD step is 71%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.0%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 26 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.003 189.7 75: (ns/day) (hour/ns) 75: Performance: 421.266 0.057 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.0%. 75: The balanceable part of the MD step is 67%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.7%. 75: 75: 75: NOTE: 15 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.011 0.006 194.8 75: (ns/day) (hour/ns) 75: Performance: 255.892 0.094 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 7.2%. 75: The balanceable part of the MD step is 58%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 4.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 188.9 75: (ns/day) (hour/ns) 75: Performance: 570.003 0.042 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 12 time 0.012 Reading energy frame 2 time 0.008 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.005 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 6 time 0.006 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Last energy frame read 4 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 5.7%. 75: The balanceable part of the MD step is 58%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 3.3%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 188.3 75: (ns/day) (hour/ns) 75: Performance: 540.427 0.044 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.5%. 75: The balanceable part of the MD step is 53%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.8%. 75: 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 188.3 75: (ns/day) (hour/ns) 75: Performance: 543.814 0.044 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 4. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 4. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 3.0%. 75: The balanceable part of the MD step is 55%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.6%. 75: 75: 75: NOTE: 40 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.012 0.006 194.5 75: (ns/day) (hour/ns) 75: Performance: 242.176 0.099 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (117 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 2.0%. 75: The balanceable part of the MD step is 69%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.3%. 75: 75: 75: NOTE: 10 % of the run time was spent in domain decomposition, 75: 3 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: NOTE: 22 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.004 191.4 75: (ns/day) (hour/ns) 75: Performance: 410.706 0.058 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 4.9%. 75: The balanceable part of the MD step is 60%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.9%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.8 75: (ns/day) (hour/ns) 75: Performance: 473.182 0.051 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was turned on during the run due to measured imbalance. 75: Average load imbalance: 4.9%. 75: The balanceable part of the MD step is 45%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 2.2%. 75: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 75: 75: 75: NOTE: 48 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.071 0.036 198.9 75: (ns/day) (hour/ns) 75: Performance: 40.884 0.587 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.7%. 75: The balanceable part of the MD step is 64%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.1%. 75: 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.253 0.251 100.9 75: (ns/day) (hour/ns) 75: Performance: 5.857 4.097 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.0%. 75: The balanceable part of the MD step is 63%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.6%. 75: 75: 75: NOTE: 27 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 189.1 75: (ns/day) (hour/ns) 75: Performance: 526.187 0.046 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 75: NVE simulation: will use the initial temperature of 68.810 K for 75: determining the Verlet buffer size 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.6%. 75: The balanceable part of the MD step is 64%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 1.0%. 75: 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 190.0 75: (ns/day) (hour/ns) 75: Performance: 485.602 0.049 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (556 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 37 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.004 191.4 75: (ns/day) (hour/ns) 75: Performance: 327.918 0.073 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 10 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 188.3 75: (ns/day) (hour/ns) 75: Performance: 615.014 0.039 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last eneOpened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-pGenerated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: rgy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 187.3 75: (ns/day) (hour/ns) 75: Performance: 670.614 0.036 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /ath/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 6 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 188.4 75: (ns/day) (hour/ns) 75: Performance: 554.334 0.043 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 183.7 75: (ns/day) (hour/ns) 75: Performance: 521.377 0.046 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (178 ms) 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 185.8 75: (ns/day) (hour/ns) 75: Performance: 495.304 0.048 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 9 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.004 189.6 75: (ns/day) (hour/ns) 75: Performance: 342.369 0.070 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: Writing final coordinates. 75: 75: NOTE: 15 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 188.7 75: (ns/day) (hour/ns) 75: Performance: 493.637 0.049 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 187.9 75: (ns/day) (hour/ns) 75: Performance: 440.656 0.054 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 6 time 0.006 Reading energy frame 11 time 0.011 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 10 time 0.010 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 16 time 0.016 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Last energy frame read 4 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: NOTE: 9 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 188.7 75: (ns/day) (hour/ns) 75: Performance: 452.719 0.053 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: 75: NOTE: 48 % of the run time was spent in domain decomposition, 75: 1 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: NOTE: 5 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.011 0.006 192.8 75: (ns/day) (hour/ns) 75: Performance: 247.041 0.097 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: For isotropic scaling we would recommend the C-rescale barostat that also 75: ensures fast relaxation without oscillations, and for anisotropic scaling 75: you likely want to use the Parrinello-Rahman barostat. 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: There was 1 warning 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.018 0.009 195.1 75: (ns/day) (hour/ns) 75: Performance: 163.665 0.147 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (89 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.161 0.081 199.5 75: (ns/day) (hour/ns) 75: Performance: 18.201 1.319 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 9 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.005 0.003 188.2 75: (ns/day) (hour/ns) 75: Performance: 553.861 0.043 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 9 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.004 0.002 187.6 75: (ns/day) (hour/ns) 75: Performance: 634.753 0.038 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: NOTE: 15 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.004 183.0 75: (ns/day) (hour/ns) 75: Performance: 413.865 0.058 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: NOTE: 14 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.004 188.2 75: (ns/day) (hour/ns) 75: Performance: 395.620 0.061 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 187.2 75: (ns/day) (hour/ns) 75: Performance: 469.647 0.051 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (160 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 9 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.005 191.0 75: (ns/day) (hour/ns) 75: Performance: 317.172 0.076 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 190.5 75: (ns/day) (hour/ns) 75: Performance: 446.533 0.054 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 15 time 0.015 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 11 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.003 190.4 75: (ns/day) (hour/ns) 75: Performance: 426.560 0.056 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: NOTE: 10 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.004 184.3 75: (ns/day) (hour/ns) 75: Performance: 403.391 0.059 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.004 189.3 75: (ns/day) (hour/ns) 75: Performance: 413.352 0.058 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 6 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.003 189.0 75: (ns/day) (hour/ns) 75: Performance: 426.915 0.056 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (74 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.005 192.3 75: (ns/day) (hour/ns) 75: Performance: 311.818 0.077 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 3 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 75: NOTE: 9 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.004 190.2 75: (ns/day) (hour/ns) 75: Performance: 330.646 0.073 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 10 time 0.010 Reading energy frame 13 time 0.013 Reading energy frame 11 time 0.011 Reading energy frame 14 time 0.014 Reading energy frame 11 time 0.011 Reading energy frame 14 time 0.014 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Last energy frame read 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 12 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.005 183.4 75: (ns/day) (hour/ns) 75: Performance: 312.221 0.077 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 16 time 0.016 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Last energy frame read 4 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.004 190.7 75: (ns/day) (hour/ns) 75: Performance: 331.937 0.072 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.004 189.6 75: (ns/day) (hour/ns) 75: Performance: 331.589 0.072 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: for current Trotter decomposition methods with vv, nsttcouple and 75: nstpcouple must be equal. Both have been reset to 75: min(nsttcouple,nstpcouple) = 2 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 75: COM removal frequency is set to (5). 75: Other settings require a global communication frequency of 2. 75: Note that this will require additional global communication steps, 75: which will reduce performance when using multiple ranks. 75: Consider setting nstcomm to a multiple of 2. 75: 75: 75: There were 4 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (89 ms) 75: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 75: 75: Writing final coordinates. 75: 75: NOTE: 11 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.009 0.005 190.5 75: (ns/day) (hour/ns) 75: Performance: 320.514 0.075 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 10 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.008 0.004 191.2 75: (ns/day) (hour/ns) 75: Performance: 346.685 0.069 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (1) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 190.4 75: (ns/day) (hour/ns) 75: Performance: 438.726 0.055 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 2 time 0.002 Reading energy frame 0 time 0.000 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.002 Reading energy frame 5 time 0.005 Reading energy frame 2 time 0.002 Reading energy frame 5 time 0.005 Reading energy frame 3 time 0.003 Reading energy frame 6 time 0.006 Reading energy frame 3 time 0.003 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 7 time 0.007 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 11 time 0.011 Reading energy frame 8 time 0.008 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: Setting nstcalcenergy (100) equal to nstenergy (4) 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: There were 2 notes 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: Writing final coordinates. 75: 75: NOTE: 10 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 188.7 75: (ns/day) (hour/ns) 75: Performance: 457.238 0.052 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: There were 2 notes 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 7 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.3 75: (ns/day) (hour/ns) 75: Performance: 431.989 0.056 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: 75: There were 2 notes 75: This run will generate roughly 0 Mb of data 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: 75: Writing final coordinates. 75: 75: NOTE: 8 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.006 0.003 189.1 75: (ns/day) (hour/ns) 75: Performance: 439.713 0.055 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 75: that with the Verlet scheme, nstlist has no effect on the accuracy of 75: your simulation. 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 75: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 75: setting nstcomm equal to nstcalcenergy for less overhead 75: 75: Generated 1 of the 1 non-bonded parameter combinations 75: 75: Excluding 1 bonded neighbours molecule type 'Argon' 75: 75: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 75: Number of degrees of freedom in T-Coupling group System is 33.00 75: 75: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 notes 75: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 75: log). 75: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 75: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 75: 75: Using 2 MPI processes 75: 75: Non-default thread affinity set, disabling internal thread affinity 75: 75: Using 1 OpenMP thread per MPI process 75: 75: starting mdrun 'Argon' 75: 16 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: NOTE: 9 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.007 0.003 189.3 75: (ns/day) (hour/ns) 75: Performance: 423.394 0.057 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 75: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 75: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (71 ms) 75: [----------] 22 tests from PropagatorsWithCoupling/PeriodicActionsTest (2762 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 22 tests from 1 test suite ran. (2836 ms total) 75: [ PASSED ] 22 tests. 75/81 Test #75: MdrunMpiCoordinationCouplingTestsTwoRanks ...... Passed 3.72 sec test 76 Start 76: MdrunMpiCoordinationConstraintsTestsOneRank 76: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-mpi-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMpiCoordinationConstraintsTestsOneRank.xml" 76: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 76: Test timeout computed to be: 1920 76: [==========] Running 10 tests from 1 test suite. 76: [----------] Global test environment set-up. 76: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 96.7 76: (ns/day) (hour/ns) 76: Performance: 557.974 0.043 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.1 76: (ns/day) (hour/ns) 76: Performance: 658.464 0.036 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.0 76: (ns/day) (hour/ns) 76: Performance: 692.046 0.035 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 94.7 76: (ns/day) (hour/ns) 76: Performance: 723.074 0.033 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.8 76: (ns/day) (hour/ns) 76: Performance: 666.370 0.036 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: NOTE: 31 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 96.4 76: (ns/day) (hour/ns) 76: Performance: 561.637 0.043 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (7585 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.4 76: (ns/day) (hour/ns) 76: Performance: 622.282 0.039 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 94.6 76: (ns/day) (hour/ns) 76: Performance: 718.353 0.033 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.001 0.001 95.9 76: (ns/day) (hour/ns) 76: Performance: 1039.412 0.023 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 94.9 76: (ns/day) (hour/ns) 76: Performance: 509.435 0.047 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.7 76: (ns/day) (hour/ns) 76: Performance: 860.899 0.028 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 4 notes 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.5 76: (ns/day) (hour/ns) 76: Performance: 902.387 0.027 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (3566 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.003 96.0 76: (ns/day) (hour/ns) 76: Performance: 584.275 0.041 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.6 76: (ns/day) (hour/ns) 76: Performance: 719.527 0.033 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.001 0.001 93.1 76: (ns/day) (hour/ns) 76: Performance: 1030.200 0.023 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.6 76: (ns/day) (hour/ns) 76: Performance: 888.846 0.027 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.001 0.002 96.3 76: (ns/day) (hour/ns) 76: Performance: 954.835 0.025 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.9 76: (ns/day) (hour/ns) 76: Performance: 784.989 0.031 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (2817 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 94.6 76: (ns/day) (hour/ns) 76: Performance: 651.088 0.037 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.7 76: (ns/day) (hour/ns) 76: Performance: 790.529 0.030 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 94.3 76: (ns/day) (hour/ns) 76: Performance: 809.646 0.030 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.4 76: (ns/day) (hour/ns) 76: Performance: 790.326 0.030 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 94.0 76: (ns/day) (hour/ns) 76: Performance: 832.400 0.029 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.2 76: (ns/day) (hour/ns) 76: Performance: 802.997 0.030 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (2738 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 96.7 76: (ns/day) (hour/ns) 76: Performance: 499.278 0.048 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.1 76: (ns/day) (hour/ns) 76: Performance: 932.152 0.026 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.4 76: (ns/day) (hour/ns) 76: Performance: 853.504 0.028 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.6 76: (ns/day) (hour/ns) 76: Performance: 728.289 0.033 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.0 76: (ns/day) (hour/ns) 76: Performance: 714.686 0.034 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.1 76: (ns/day) (hour/ns) 76: Performance: 722.481 0.033 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2955 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 97.1 76: (ns/day) (hour/ns) 76: Performance: 720.200 0.033 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 97.3 76: (ns/day) (hour/ns) 76: Performance: 725.800 0.033 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.8 76: (ns/day) (hour/ns) 76: Performance: 874.215 0.027 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.1 76: (ns/day) (hour/ns) 76: Performance: 713.197 0.034 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.0 76: (ns/day) (hour/ns) 76: Performance: 797.591 0.030 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.6 76: (ns/day) (hour/ns) 76: Performance: 758.787 0.032 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3308 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.003 95.7 76: (ns/day) (hour/ns) 76: Performance: 584.109 0.041 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.6 76: (ns/day) (hour/ns) 76: Performance: 703.344 0.034 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.4 76: (ns/day) (hour/ns) 76: Performance: 803.206 0.030 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 95.9 76: (ns/day) (hour/ns) 76: Performance: 717.767 0.033 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.2 76: (ns/day) (hour/ns) 76: Performance: 683.220 0.035 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 96.6 76: (ns/day) (hour/ns) 76: Performance: 727.686 0.033 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (3400 ms) 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 98.2 76: (ns/day) (hour/ns) 76: Performance: 475.575 0.050 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 98.2 76: (ns/day) (hour/ns) 76: Performance: 569.740 0.042 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 97.8 76: (ns/day) (hour/ns) 76: Performance: 655.522 0.037 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 97.4 76: (ns/day) (hour/ns) 76: Performance: 542.067 0.044 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.003 98.2 76: (ns/day) (hour/ns) 76: Performance: 583.721 0.041 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: NVE simulation: will use the initial temperature of 398.997 K for 76: determining the Verlet buffer size 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 4. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 4. 76: 76: 76: There were 5 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: NOTE: 11 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 97.9 76: (ns/day) (hour/ns) 76: Performance: 597.188 0.040 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (4217 ms) 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 98.4 76: (ns/day) (hour/ns) 76: Performance: 446.808 0.054 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 notes 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.003 0.003 97.7 76: (ns/day) (hour/ns) 76: Performance: 570.425 0.042 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.2 76: (ns/day) (hour/ns) 76: Performance: 406.962 0.059 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 97.6 76: (ns/day) (hour/ns) 76: Performance: 620.527 0.039 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.4 76: (ns/day) (hour/ns) 76: Performance: 378.275 0.063 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 76: COM removal frequency is set to (5). 76: Other settings require a global communication frequency of 2. 76: Note that this will require additional global communication steps, 76: which will reduce performance when using multiple ranks. 76: Consider setting nstcomm to a multiple of 2. 76: 76: 76: There were 4 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (7519 ms) 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.011 0.011 99.4 76: (ns/day) (hour/ns) 76: Performance: 137.526 0.175 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 76: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.011 0.011 99.4 76: (ns/day) (hour/ns) 76: Performance: 129.558 0.185 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (1) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.5 76: (ns/day) (hour/ns) 76: Performance: 336.626 0.071 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: Setting nstcalcenergy (100) equal to nstenergy (4) 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.002 0.002 97.6 76: (ns/day) (hour/ns) 76: Performance: 643.471 0.037 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.5 76: (ns/day) (hour/ns) 76: Performance: 344.784 0.070 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.004 0.004 98.4 76: (ns/day) (hour/ns) 76: Performance: 359.848 0.067 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 76: that with the Verlet scheme, nstlist has no effect on the accuracy of 76: your simulation. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 76: setting nstcomm equal to nstcalcenergy for less overhead 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 notes 76: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 76: log). 76: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 76: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 76: 76: Using 1 MPI process 76: 76: Non-default thread affinity set, disabling internal thread affinity 76: 76: Using 1 OpenMP thread 76: 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (6279 ms) 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.011 0.011 99.4 76: (ns/day) (hour/ns) 76: Performance: 136.902 0.175 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 76: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 76: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (44401 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 10 tests from 1 test suite ran. (44483 ms total) 76: [ PASSED ] 10 tests. 76/81 Test #76: MdrunMpiCoordinationConstraintsTestsOneRank .... Passed 45.05 sec test 77 Start 77: MdrunMpiCoordinationConstraintsTestsTwoRanks 77: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-mpi-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunMpiCoordinationConstraintsTestsTwoRanks.xml" 77: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 77: Test timeout computed to be: 1920 77: [==========] Running 10 tests from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.3%. 77: The balanceable part of the MD step is 11%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.1%. 77: 77: 77: NOTE: 7 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.022 0.011 198.2 77: (ns/day) (hour/ns) 77: Performance: 131.078 0.183 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 0.8%. 77: The balanceable part of the MD step is 13%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.1%. 77: 77: 77: NOTE: 10 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.013 0.006 196.9 77: (ns/day) (hour/ns) 77: Performance: 226.276 0.106 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB got disabled because it was unsuitable to use. 77: Average load imbalance: 3.8%. 77: The balanceable part of the MD step is 55%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 2.1%. 77: 77: 77: NOTE: 3 % of the run time was spent in domain decomposition, 77: 34 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: NOTE: 9 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.012 0.006 196.4 77: (ns/day) (hour/ns) 77: Performance: 231.306 0.104 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.2%. 77: The balanceable part of the MD step is 54%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.2%. 77: 77: 77: NOTE: 67 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.034 0.017 198.4 77: (ns/day) (hour/ns) 77: Performance: 84.801 0.283 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.6%. 77: The balanceable part of the MD step is 54%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.4%. 77: 77: 77: NOTE: 47 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.029 0.015 198.6 77: (ns/day) (hour/ns) 77: Performance: 100.840 0.238 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.5%. 77: The balanceable part of the MD step is 53%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.3%. 77: 77: 77: NOTE: 89 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.040 0.020 198.5 77: (ns/day) (hour/ns) 77: Performance: 73.070 0.328 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (6955 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.3%. 77: The balanceable part of the MD step is 63%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.8%. 77: 77: 77: NOTE: 44 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.022 0.011 198.1 77: (ns/day) (hour/ns) 77: Performance: 130.719 0.184 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.8%. 77: The balanceable part of the MD step is 58%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.1%. 77: 77: 77: NOTE: 42 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.013 0.007 196.9 77: (ns/day) (hour/ns) 77: Performance: 223.745 0.107 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.9%. 77: The balanceable part of the MD step is 57%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.1%. 77: 77: 77: NOTE: 28 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 182.8 77: (ns/day) (hour/ns) 77: Performance: 709.419 0.034 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.7%. 77: The balanceable part of the MD step is 57%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.0%. 77: 77: 77: NOTE: 78 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.032 0.030 106.9 77: (ns/day) (hour/ns) 77: Performance: 49.016 0.490 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.8%. 77: The balanceable part of the MD step is 57%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.0%. 77: 77: 77: NOTE: 30 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 189.8 77: (ns/day) (hour/ns) 77: Performance: 700.306 0.034 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.0%. 77: The balanceable part of the MD step is 56%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.1%. 77: 77: 77: NOTE: 44 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.013 0.007 196.5 77: (ns/day) (hour/ns) 77: Performance: 221.369 0.108 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (6915 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.022 0.011 198.2 77: (ns/day) (hour/ns) 77: Performance: 132.419 0.181 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: Writing final coordinates. 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.004 0.002 191.2 77: (ns/day) (hour/ns) 77: Performance: 661.150 0.036 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: NOTE: 46 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.051 0.026 198.9 77: (ns/day) (hour/ns) 77: Performance: 57.532 0.417 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: 77: NOTE: 55 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.036 0.018 198.2 77: (ns/day) (hour/ns) 77: Performance: 80.526 0.298 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: NOTE: 35 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.042 0.021 198.4 77: (ns/day) (hour/ns) 77: Performance: 68.907 0.348 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: 77: NOTE: 25 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.012 0.006 196.2 77: (ns/day) (hour/ns) 77: Performance: 233.577 0.103 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (7155 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.030 0.015 198.6 77: (ns/day) (hour/ns) 77: Performance: 96.144 0.250 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.007 0.004 194.2 77: (ns/day) (hour/ns) 77: Performance: 395.036 0.061 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE: 28 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.042 0.021 198.5 77: (ns/day) (hour/ns) 77: Performance: 69.182 0.347 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.007 0.003 194.2 77: (ns/day) (hour/ns) 77: Performance: 421.554 0.057 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: 77: NOTE: 32 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.020 0.010 197.0 77: (ns/day) (hour/ns) 77: Performance: 143.435 0.167 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: NOTE: 21 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.013 0.006 196.7 77: (ns/day) (hour/ns) 77: Performance: 230.002 0.104 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3731 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: NOTE: 32 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.026 0.013 197.6 77: (ns/day) (hour/ns) 77: Performance: 112.396 0.214 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.021 0.011 198.1 77: (ns/day) (hour/ns) 77: Performance: 139.374 0.172 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE: 46 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.052 0.026 198.8 77: (ns/day) (hour/ns) 77: Performance: 56.686 0.423 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: NOTE: 29 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.069 0.035 199.3 77: (ns/day) (hour/ns) 77: Performance: 42.541 0.564 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.007 0.004 194.8 77: (ns/day) (hour/ns) 77: Performance: 388.228 0.062 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.021 0.010 197.9 77: (ns/day) (hour/ns) 77: Performance: 139.893 0.172 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (4715 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.013 0.007 197.5 77: (ns/day) (hour/ns) 77: Performance: 216.476 0.111 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.013 0.007 197.6 77: (ns/day) (hour/ns) 77: Performance: 225.082 0.107 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: Writing final coordinates. 77: 77: NOTE: 25 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.007 0.004 195.3 77: (ns/day) (hour/ns) 77: Performance: 391.659 0.061 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.012 0.006 196.3 77: (ns/day) (hour/ns) 77: Performance: 241.805 0.099 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.013 0.006 197.3 77: (ns/day) (hour/ns) 77: Performance: 228.445 0.105 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.021 0.010 198.2 77: (ns/day) (hour/ns) 77: Performance: 141.470 0.170 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (4467 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.022 0.011 198.1 77: (ns/day) (hour/ns) 77: Performance: 131.789 0.182 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: Writing final coordinates. 77: 77: NOTE: 32 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.021 0.011 198.3 77: (ns/day) (hour/ns) 77: Performance: 138.481 0.173 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE: 10 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.044 0.022 198.7 77: (ns/day) (hour/ns) 77: Performance: 66.783 0.359 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.021 0.011 198.1 77: (ns/day) (hour/ns) 77: Performance: 136.873 0.175 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.005 0.002 192.4 77: (ns/day) (hour/ns) 77: Performance: 592.906 0.040 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (6283 ms) 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.021 0.011 198.2 77: (ns/day) (hour/ns) 77: Performance: 139.797 0.172 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 0.6%. 77: The balanceable part of the MD step is 67%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.4%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.016 0.012 134.5 77: (ns/day) (hour/ns) 77: Performance: 126.751 0.189 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.5%. 77: The balanceable part of the MD step is 29%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.4%. 77: 77: 77: NOTE: 5 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.010 0.005 194.1 77: (ns/day) (hour/ns) 77: Performance: 297.707 0.081 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 2.1%. 77: The balanceable part of the MD step is 22%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.5%. 77: 77: 77: NOTE: 22 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.008 0.004 193.2 77: (ns/day) (hour/ns) 77: Performance: 339.455 0.071 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 11.7%. 77: The balanceable part of the MD step is 11%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 1.3%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.014 0.007 194.9 77: (ns/day) (hour/ns) 77: Performance: 204.579 0.117 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.1%. 77: The balanceable part of the MD step is 65%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.7%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.022 0.011 196.8 77: (ns/day) (hour/ns) 77: Performance: 131.482 0.183 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: NVE simulation: will use the initial temperature of 398.997 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 notes 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: 77: Dynamic load balancing report: 77: DLB was off during the run due to low measured imbalance. 77: Average load imbalance: 1.9%. 77: The balanceable part of the MD step is 12%, load imbalance is computed from this. 77: Part of the total run time spent waiting due to load imbalance: 0.2%. 77: 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.014 0.007 195.1 77: (ns/day) (hour/ns) 77: Performance: 210.929 0.114 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (4830 ms) 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.016 0.008 195.2 77: (ns/day) (hour/ns) 77: Performance: 182.115 0.132 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 77: Writing final coordinates. 77: 77: NOTE: 7 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.008 0.004 190.6 77: (ns/day) (hour/ns) 77: Performance: 370.517 0.065 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: Writing final coordinates. 77: 77: NOTE: 6 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.008 0.004 192.2 77: (ns/day) (hour/ns) 77: Performance: 342.227 0.070 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.012 0.006 193.4 77: (ns/day) (hour/ns) 77: Performance: 229.227 0.105 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.009 0.005 191.0 77: (ns/day) (hour/ns) 77: Performance: 301.067 0.080 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 77: COM removal frequency is set to (5). 77: Other settings require a global communication frequency of 2. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 2. 77: 77: 77: There were 4 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (5125 ms) 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: NOTE: 35 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.069 0.035 198.4 77: (ns/day) (hour/ns) 77: Performance: 42.514 0.565 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 77: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: NOTE: 7 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.007 0.004 190.7 77: (ns/day) (hour/ns) 77: Performance: 386.353 0.062 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE: 32 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.064 0.049 131.9 77: (ns/day) (hour/ns) 77: Performance: 30.058 0.798 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: Writing final coordinates. 77: 77: NOTE: 33 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.038 0.019 198.0 77: (ns/day) (hour/ns) 77: Performance: 76.167 0.315 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: NOTE: 26 % of the run time was spent communicating energies, 77: you might want to increase some nst* mdp options 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.062 0.031 198.5 77: (ns/day) (hour/ns) 77: Performance: 46.848 0.512 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.023 0.012 196.2 77: (ns/day) (hour/ns) 77: Performance: 127.118 0.189 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Generated 330891 of the 330891 non-bonded parameter combinations 77: Generating 1-4 interactions: fudge = 0.5 77: 77: Generated 330891 of the 330891 1-4 parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: Number of degrees of freedom in T-Coupling group System is 27.00 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 77: You are using a plain Coulomb cut-off, which might produce artifacts. 77: You might want to consider using PME electrostatics. 77: 77: 77: 77: This run will generate roughly 0 Mb of data 77: 77: There were 3 notes 77: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 77: log). 77: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 77: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 77: 77: Using 2 MPI processes 77: 77: Non-default thread affinity set, disabling internal thread affinity 77: 77: Using 1 OpenMP thread per MPI process 77: 77: starting mdrun 'spc2' 77: 16 steps, 0.0 ps. 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.022 0.011 196.0 77: (ns/day) (hour/ns) 77: Performance: 127.946 0.188 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 77: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (6658 ms) 77: [----------] 10 tests from PropagatorsWithConstraints/PeriodicActionsTest (56863 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 10 tests from 1 test suite ran. (57074 ms total) 77: [ PASSED ] 10 tests. 77/81 Test #77: MdrunMpiCoordinationConstraintsTestsTwoRanks ... Passed 57.87 sec test 78 Start 78: MdrunFEPTests 78: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunFEPTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 10 tests from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 10 tests from EquivalentToReference/FreeEnergyReferenceTest 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI process 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -528385 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.570 0.285 199.9 78: (ns/day) (hour/ns) 78: Performance: 6.366 3.770 78: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (803 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI process 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to 1069414875 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.242 0.121 199.8 78: (ns/day) (hour/ns) 78: Performance: 14.980 1.602 78: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (212 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: With PME there is a minor soft core effect present at the cut-off, 78: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 78: energy conservation, but usually other effects dominate. With a common 78: sigma value of 0.34 nm the fraction of the particle-particle potential at 78: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 4 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI process 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -542786627 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.174 0.087 199.7 78: (ns/day) (hour/ns) 78: Performance: 20.798 1.154 78: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (154 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 78: For proper sampling of the (nearly) decoupled state, stochastic dynamics 78: should be used 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 78: and vdw_modifier=Force-switch 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 4 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI process 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 100 steps, 0.1 ps. 78: Setting the LD random seed to 1778212831 78: 78: Generated 153 of the 153 non-bonded parameter combinations 78: 78: Generated 153 of the 153 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: 78: Coupling 1 copies of molecule type 'ASN' 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 2.191 1.095 200.0 78: (ns/day) (hour/ns) 78: Performance: 7.966 3.013 78: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (1186 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: WARNING 2 [file topol.top, line 72]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 3 [file topol.top, line 73]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 4 [file topol.top, line 98]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 5 [file topol.top, line 99]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 6 [file topol.top, line 100]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 7 [file topol.top, line 101]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 8 [file topol.top, line 111]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 9 [file topol.top, line 112]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 10 [file topol.top, line 113]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 11 [file topol.top, line 114]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 2 notes 78: 78: There were 11 warnings 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI process 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to 2145369597 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.251 0.626 200.0 78: (ns/day) (hour/ns) 78: Performance: 2.900 8.277 78: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (785 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: 78: WARNING 2 [file topol.top, line 72]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 3 [file topol.top, line 73]: 78: No default Bond types for perturbed atoms, using normal values 78: 78: 78: WARNING 4 [file topol.top, line 98]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 5 [file topol.top, line 99]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 6 [file topol.top, line 100]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 7 [file topol.top, line 101]: 78: No default Angle types for perturbed atoms, using normal values 78: 78: 78: WARNING 8 [file topol.top, line 111]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 9 [file topol.top, line 112]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 10 [file topol.top, line 113]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: 78: WARNING 11 [file topol.top, line 114]: 78: No default Ryckaert-Bell. types for perturbed atoms, using normal values 78: 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: Removing center of mass motion in the presence of position restraints 78: might cause artifacts. When you are using position restraints to 78: equilibrate a macro-molecule, the artifacts are usually negligible. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There were 11 warnings 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI process 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to 2147430202 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.797 0.399 199.9 78: (ns/day) (hour/ns) 78: Performance: 4.549 5.276 78: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (543 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 2 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI process 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -604774915 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.331 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.88 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.091 0.045 199.5 78: (ns/day) (hour/ns) 78: Performance: 39.958 0.601 78: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (129 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There was 1 note 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI process 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.079 0.040 199.4 78: (ns/day) (hour/ns) 78: Performance: 45.669 0.526 78: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -642908967 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between excluded atoms is 0.331 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.88 78: 78: This run will generate roughly 0 Mb of data 78: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (85 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: With PME there is a minor soft core effect present at the cut-off, 78: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 78: energy conservation, but usually other effects dominate. With a common 78: sigma value of 0.34 nm the fraction of the particle-particle potential at 78: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI process 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to -1628078467 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.164 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.94 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.218 0.109 199.8 78: (ns/day) (hour/ns) 78: Performance: 16.622 1.444 78: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (158 ms) 78: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: With PME there is a minor soft core effect present at the cut-off, 78: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 78: energy conservation, but usually other effects dominate. With a common 78: sigma value of 0.34 nm the fraction of the particle-particle potential at 78: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 78: 78: 78: WARNING 1 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: The Berendsen thermostat does not generate the correct kinetic energy 78: distribution, and should not be used for new production simulations (in 78: our opinion). We would recommend the V-rescale thermostat. 78: 78: Generating 1-4 interactions: fudge = 0.5 78: Number of degrees of freedom in T-Coupling group System is 355.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 78: For free energy simulations, the optimal load limit increases from 0.5 to 78: 0.667 78: 78: 78: 78: There were 3 notes 78: 78: There was 1 warning 78: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 78: log). 78: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 78: Changing nstlist from 10 to 100, rlist from 1 to 1 78: 78: Using 1 MPI process 78: Using 2 OpenMP threads 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'AA' 78: 20 steps, 0.0 ps. 78: Setting the LD random seed to 1039138271 78: 78: Generated 136 of the 136 non-bonded parameter combinations 78: 78: Generated 136 of the 136 1-4 parameter combinations 78: 78: Excluding 3 bonded neighbours molecule type 'ASN' 78: 78: turning H bonds into constraints... 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: turning H bonds into constraints... 78: Analysing residue names: 78: There are: 1 Protein residues 78: There are: 56 Water residues 78: Analysing Protein... 78: 78: The largest distance between non-perturbed excluded atoms is 0.172 nm 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 0.88 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.107 0.054 199.6 78: (ns/day) (hour/ns) 78: Performance: 33.815 0.710 78: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (103 ms) 78: [----------] 10 tests from EquivalentToReference/FreeEnergyReferenceTest (4165 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 10 tests from 1 test suite ran. (4308 ms total) 78: [ PASSED ] 10 tests. 78/81 Test #78: MdrunFEPTests .................................. Passed 5.32 sec test 79 Start 79: MdrunPullTests 79: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunPullTests.xml" 79: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 79: Test timeout computed to be: 600 79: [==========] Running 4 tests from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 4 tests from PullTest/PullIntegrationTest 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1293.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.122 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.575 nm 0.600 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.095 0.047 199.5 79: (ns/day) (hour/ns) 79: Performance: 38.216 0.628 79: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (643 ms) 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1293.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.122 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.301 nm 0.400 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.070 0.035 199.4 79: (ns/day) (hour/ns) 79: Performance: 51.989 0.462 79: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (471 ms) 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Pull group 3 'r_3' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1292.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.357 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.575 nm 0.500 nm 79: 1 3 2 79: 3 3 8 0.331 nm 0.400 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 15 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.085 0.043 199.5 79: (ns/day) (hour/ns) 79: Performance: 42.348 0.567 79: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (463 ms) 79: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 79: Generating 1-4 interactions: fudge = 0.5 79: Pull group 1 'r_1' has 3 atoms 79: Pull group 2 'r_2' has 3 atoms 79: Number of degrees of freedom in T-Coupling group System is 1293.00 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 303.122 K for 79: determining the Verlet buffer size 79: 79: Pull group natoms pbc atom distance at start reference at t=0 79: 1 3 2 79: 2 3 5 0.575 nm 0.000 nm 79: 1 3 2 79: 2 3 5 0.050 nm 0.000 nm 79: 79: There was 1 note 79: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 79: log). 79: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 2 OpenMP threads 79: 79: 79: NOTE: The number of threads is not equal to the number of (logical) cpus 79: and the -pin option is set to auto: will not pin threads to cpus. 79: This can lead to significant performance degradation. 79: Consider using -pin on (and -pinoffset in case you run multiple jobs). 79: starting mdrun 'spc2' 79: 20 steps, 0.0 ps. 79: Generated 330891 of the 330891 non-bonded parameter combinations 79: 79: Generated 330891 of the 330891 1-4 parameter combinations 79: 79: Excluding 2 bonded neighbours molecule type 'SOL' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 30 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.069 0.035 199.3 79: (ns/day) (hour/ns) 79: Performance: 52.209 0.460 79: Opened /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (480 ms) 79: [----------] 4 tests from PullTest/PullIntegrationTest (2060 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 4 tests from 1 test suite ran. (2196 ms total) 79: [ PASSED ] 4 tests. 79/81 Test #79: MdrunPullTests ................................. Passed 3.38 sec test 80 Start 80: MdrunSimulatorComparison 80: Test command: /build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunSimulatorComparison.xml" 80: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 80: Test timeout computed to be: 600 80: [==========] Running 0 tests from 0 test suites. 80: [==========] 0 tests from 0 test suites ran. (0 ms total) 80: [ PASSED ] 0 tests. 80: 80: YOU HAVE 82 DISABLED TESTS 80: 80/81 Test #80: MdrunSimulatorComparison ....................... Passed 1.19 sec test 81 Start 81: MdrunVirtualSiteTests 81: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2022.5/build/mpi/bin/mdrun-vsites-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2022.5/build/mpi/Testing/Temporary/MdrunVirtualSiteTests.xml" 81: Working Directory: /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests 81: Test timeout computed to be: 600 81: [==========] Running 37 tests from 2 test suites. 81: [----------] Global test environment set-up. 81: [----------] 1 test from VirtualSiteVelocityTest 81: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 81: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 81: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 81: 81: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (63 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 81: Reading virtual site types... 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 5.9%. 81: The balanceable part of the MD step is 50%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.9%. 81: 81: 81: NOTE: 47 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.023 0.012 198.0 81: (ns/day) (hour/ns) 81: Performance: 65.868 0.364 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: trr version: GMX_trn_file (single precision) 81: 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: trr version: GMX_trn_file (single precision) 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: This run will generate roughly 0 Mb of data 81: Reading virtual site types... 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 6.7%. 81: The balanceable part of the MD step is 48%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 3.2%. 81: 81: 81: NOTE: 30 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 189.1 81: (ns/day) (hour/ns) 81: Performance: 372.423 0.064 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading virtual site types... 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (36 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: NOTE: 31 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 189.3 81: (ns/day) (hour/ns) 81: Performance: 410.405 0.058 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading virtual site types... 81: 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (36 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Reading virtual site types... 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (48 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: 81: NOTE: 46 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.010 197.4 81: (ns/day) (hour/ns) 81: Performance: 74.134 0.324 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: NOTE: 30 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.003 0.002 187.9 81: (ns/day) (hour/ns) 81: Performance: 431.443 0.056 81: Reading virtual site types... 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (63 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 5 notes 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: Reading virtual site types... 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: NOTE: 30 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 190.2 81: (ns/day) (hour/ns) 81: Performance: 393.022 0.061 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (107 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 5 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: 81: Writing final coordinates. 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 189.4 81: (ns/day) (hour/ns) 81: Performance: 379.199 0.063 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading virtual site types... 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (43 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 5 notes 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: NOTE: 76 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.035 0.022 161.6 81: (ns/day) (hour/ns) 81: Performance: 35.449 0.677 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (80 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: NVE simulation with an initial temperature of zero: will use a Verlet 81: buffer of 10%. Check your energy drift! 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: 81: Dynamic load balancing report: 81: DLB was off during the run due to low measured imbalance. 81: Average load imbalance: 4.9%. 81: The balanceable part of the MD step is 44%, load imbalance is computed from this. 81: Part of the total run time spent waiting due to load imbalance: 2.2%. 81: 81: 81: NOTE: 28 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 190.7 81: (ns/day) (hour/ns) 81: Performance: 339.703 0.071 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (54 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: 81: NOTE: 31 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 189.3 81: (ns/day) (hour/ns) 81: Performance: 402.628 0.060 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading virtual site types... 81: 81: Reading virtual site types... 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (48 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (72 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 81: Reading virtual site types... 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: 81: NOTE: 31 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.012 33.9 81: (ns/day) (hour/ns) 81: Performance: 63.712 0.377 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (99 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 81: Reading virtual site types... 81: 81: NOTE: 15 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.014 29.2 81: (ns/day) (hour/ns) 81: Performance: 54.693 0.439 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: 81: NOTE: 87 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.024 0.022 109.8 81: (ns/day) (hour/ns) 81: Performance: 35.245 0.681 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading virtual site types... 81: Reading virtual site types... 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (71 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: NOTE: 31 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 190.7 81: (ns/day) (hour/ns) 81: Performance: 383.976 0.063 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading virtual site types... 81: 81: Reading virtual site types... 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (39 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: NOTE: 29 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 191.3 81: (ns/day) (hour/ns) 81: Performance: 392.148 0.061 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading virtual site types... 81: 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (63 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.709 nm, buffer size 0.009 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.709 to 0.873 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: NOTE: 30 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 192.0 81: (ns/day) (hour/ns) 81: Performance: 373.425 0.064 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading virtual site types... 81: 81: Reading virtual site types... 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (48 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: 81: Writing final coordinates. 81: 81: NOTE: 58 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.036 0.018 198.9 81: (ns/day) (hour/ns) 81: Performance: 42.533 0.564 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading virtual site types... 81: Reading virtual site types... 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (43 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Reading virtual site types... 81: 81: NOTE: 30 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.004 0.002 190.9 81: (ns/day) (hour/ns) 81: Performance: 387.696 0.062 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading virtual site types... 81: 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (48 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 3 of the 6 non-bonded parameter combinations 81: 81: Excluding 3 bonded neighbours molecule type 'VSTEST' 81: 81: Cleaning up constraints and constant bonded interactions with virtual sites 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.721 nm, buffer size 0.021 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.721 nm, buffer size 0.021 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 45.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: There are 6 non-linear virtual site constructions. Their contribution to 81: the energy error is approximated. In most cases this does not affect the 81: error significantly. 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 notes 81: Compiled SIMD: SSE4.1, but for this host/run AVX_256 might be better (see 81: log). 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.721 to 0.779 81: 81: Using 2 MPI processes 81: 81: Non-default thread affinity set, disabling internal thread affinity 81: 81: Using 1 OpenMP thread per MPI process 81: 81: starting mdrun 'Virtual sites test system in vacuo' 81: 8 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: NOTE: 30 % of the run time was spent communicating energies, 81: you might want to increase some nst* mdp options 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.003 0.002 189.4 81: (ns/day) (hour/ns) 81: Performance: 426.897 0.056 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading virtual site types... 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (36 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 81: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 81: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 81: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (1181 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 37 tests from 2 test suites ran. (1376 ms total) 81: [ PASSED ] 37 tests. 81: Reading virtual site types... 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: Reading file /build/reproducible-path/gromacs-2022.5/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2022.5-Debian_2022.5_2 (single precision) 81: 81: 81/81 Test #81: MdrunVirtualSiteTests .......................... Passed 2.24 sec 100% tests passed, 0 tests failed out of 81 Label Time Summary: GTest = 238.08 sec*proc (79 tests) IntegrationTest = 62.52 sec*proc (23 tests) MpiTest = 138.02 sec*proc (19 tests) QuickGpuTest = 21.27 sec*proc (15 tests) SlowTest = 145.16 sec*proc (13 tests) UnitTest = 30.40 sec*proc (43 tests) Total Test time (real) = 238.29 sec touch build-mpi dh_testdir (mkdir -p build/documentation ; cd build/documentation; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2022.5/build/documentation/lib \ cmake /build/reproducible-path/gromacs-2022.5 -DCMAKE_BUILD_TYPE=Debug -DGMX_OPENMP=OFF -DGMX_SIMD=None \ -DGMX_GPU=OFF -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DGMX_BUILD_MANUAL=ON \ -DGMX_BUILD_HELP=ON -DGMX_VERSION_STRING_OF_FORK="Debian-2022.5-2") -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Python3_LIBRARIES Development Development.Module Development.Embed) (found suitable version "3.11.2", minimum required is "3.7") -- Performing Test CFLAGS_PRAGMA -- Performing Test CFLAGS_PRAGMA - Success -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_PRAGMA -- Performing Test CXXFLAGS_PRAGMA - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Using default binary suffix: "" -- Using default library suffix: "" -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - AMD -- Detected build CPU brand - AMD Opteron 62xx class CPU -- Detected build CPU family - 21 -- Detected build CPU model - 1 -- Detected build CPU stepping - 2 -- Detected build CPU features - aes amd apic avx clfsh cmov cx8 cx16 lahf misalignsse mmx msr pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/x86_64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/x86_64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "5.3.0", minimum required is "1.6.1") found components: pygments -- Found LATEX: /usr/bin/latex -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed -- Found Python: /usr/bin/python3 (found version "3.11.2") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_NO_REDUNDANT_MOVE -- Performing Test HAS_NO_REDUNDANT_MOVE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done -- 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/external/zlib/zutil.c make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/mdrun/nonbonded_bench.cpp [ 1%] Built target lmfit_objlib /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/programs /build/reproducible-path/gromacs-2022.5/build/documentation /build/reproducible-path/gromacs-2022.5/build/documentation/src/programs /build/reproducible-path/gromacs-2022.5/build/documentation/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/docs /build/reproducible-path/gromacs-2022.5/build/documentation /build/reproducible-path/gromacs-2022.5/build/documentation/docs /build/reproducible-path/gromacs-2022.5/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src -isystem /build/reproducible-path/gromacs-2022.5/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o -MF CMakeFiles/view_objlib.dir/view/view.cpp.o.d -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/programs/view/view.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/sgangle.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/sgangle.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/plots/decomp.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/plots/decomp.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/plots/dih.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/plots/dih.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/plots/drift-all.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/plots/drift-all.png [ 2%] Built target thread_mpi /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/plots/f-angle.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/plots/f-angle.png make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/docs /build/reproducible-path/gromacs-2022.5/build/documentation /build/reproducible-path/gromacs-2022.5/build/documentation/docs /build/reproducible-path/gromacs-2022.5/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake --color= cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/plots/f-bond.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/plots/f-bond.png make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/sgangle.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/sgangle.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2022.5/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2022.5/docs/conf.cmakein.py -D VERSION_OUT=/build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/conf.py -D CMAKE_MINIMUM_REQUIRED_VERSION=3.16.3 -D EXPECTED_DOXYGEN_VERSION=1.8.5 -D EXPECTED_SPHINX_VERSION=1.6.1 -D GMX_ADMIN_DIR=/build/reproducible-path/gromacs-2022.5/admin -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=This is not a release build of GROMACS, so please reference one of the GROMACS papers and the base release of the manual." -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D "GMX_SOURCE_DOI_STRING=This is not a release build of GROMACS. Please reference one of the GROMACS papers, as well as the base release that this version is built from. Also, please state what modifcations have been performed or where the version was sourced from." -D GMXAPI_PYTHON_STAGING_DIR= -D IMAGE_CONVERT_STRING=possible -D REGRESSIONTEST_VERSION=2022.5 -D REQUIRED_CUDA_COMPUTE_CAPABILITY=3.5 -D REQUIRED_CUDA_VERSION=11.0 -D REQUIRED_OPENCL_MIN_VERSION= -D REGRESSIONTEST_MD5SUM_STRING=unknown -D RELENG_PATH= -D SOURCE_MD5SUM=unknown -D SPHINX_EXTENSION_PATH=/build/reproducible-path/gromacs-2022.5/docs -D "GMX_CURRENT_CONTRIBUTORS_STRING=Mark Abraham, Andrey Alekseenko, Cathrine Bergh, Christian Blau, Eliane Briand, Kevin Boyd, Oliver Fleetwood, Stefan Fleischmann, Vytas Gapsys, Gaurav Garg, Gilles Gouaillardet, Alan Gray, Victor Holanda, M. Eric Irrgang, Joe Jordan, Christoph Junghans, Prashanth Kanduri, Sebastian Kehl, Sebastian Keller, Carsten Kutzner, Magnus Lundborg, Pascal Merz, Dmitry Morozov, Szilard Pall, Roland Schulz, Michael Shirts, David van der Spoel, Alessandra Villa, Sebastian Wingbermuehle, Artem Zhmurov" -D "GMX_PREVIOUS_CONTRIBUTORS_STRING=Emile Apol, Rossen Apostolov, James Barnett, Herman J.C. Berendsen, Par Bjelkmar, Viacheslav Bolnykh, Aldert van Buuren, Carlo Camilloni, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Bert de Groot, Anca Hamuraru, Vincent Hindriksen, Aleksei Iupinov, Dimitrios Karkoulis, Peter Kasson, Jiri Kraus, Per Larsson, Justin A. Lemkul, Viveca Lindahl, Erik Marklund, Pieter Meulenhoff, Vedran Miletic, Teemu Murtola, Sander Pronk, Alexey Shvetsov, Alfons Sijbers, Peter Tieleman, Jon Vincent, Teemu Virolainen, Christian Wennberg, Maarten Wolf" -D "GMX_CURRENT_PROJECT_LEADERS_STRING=Paul Bauer, Berk Hess, Erik Lindahl" -P /build/reproducible-path/gromacs-2022.5/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/conf.py cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/index.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/index.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/download.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/download.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -fPIC -std=c++11 -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o -MF CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/external/muparser/src/muParserBytecode.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/links.dat /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/links.dat cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/build-system.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/build-system.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/plots/fp-highres.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/plots/fp-highres.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/change-management.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/change-management.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/plots/int-mat.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/plots/int-mat.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/plots/mdpar.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/plots/mdpar.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/commitstyle.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/commitstyle.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/containers.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/containers.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/plots/parsort.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/plots/parsort.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/documentation-generation.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/documentation-generation.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/contribute.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/contribute.rst [ 4%] Built target tng_io_zlib cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/plots/ring.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/plots/ring.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/doxygen.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/doxygen.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/error-handling.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/error-handling.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/formatting.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/formatting.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/plots/shiftf.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/plots/shiftf.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/gitlab-ci.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/gitlab-ci.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/algorithms/plots/dd-cells.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/dd-cells.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/algorithms/plots/dd-tric.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/dd-tric.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/gmxtree.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/gmxtree.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/includestyle.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/includestyle.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/index.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/index.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/algorithms/plots/flowchart.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/flowchart.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/dev-manual/infrastructure.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/dev-manual/infrastructure.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/algorithms/plots/free1.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/chain.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/functions/plots/chain.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/release-notes/index.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/release-notes/index.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/dummies.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch 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/build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/fig-04.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/functions/plots/fig-04.png cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/release-notes/2022/major/performance.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/release-notes/2022/major/performance.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/release-notes/2022/major/tools.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/release-notes/2022/major/tools.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/f-imps.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input//reference-manual/functions/plots/f-imps.png [ 4%] Built target linearalgebra cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/release-notes/2022/major/bugs-fixed.rst /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/release-notes/2022/major/bugs-fixed.rst cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy 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/build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/mpmd-pme.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/algorithms/plots/nstric.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/nstric.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/algorithms/plots/par-lincs2.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/par-lincs2.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/algorithms/plots/pbctric.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/pbctric.pdf make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/algorithms/plots/rhododec.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/rhododec.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/algorithms/plots/truncoct.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/truncoct.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/algorithms/plots/verlet-drift.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/verlet-drift.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/angle.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/angle.pdf [ 4%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/bstretch.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/bstretch.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy 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/build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/f-lj.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-lj.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/f-morse.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-morse.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/f-pr.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-pr.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-image-conversion-timestamp.txt cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/f-rbs.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/f-rbs.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/ring-imp.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/ring-imp.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/softcore.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/softcore.pdf make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/gapsys-sc.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/gapsys-sc.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/subst-im.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/subst-im.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/tetra-im.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/tetra-im.pdf [ 10%] Built target sphinx-image-conversion cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/vcrf.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/vcrf.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/functions/plots/vsite-4fdn.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/functions/plots/vsite-4fdn.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy 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/build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/dih-def.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/distm.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/distm.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/dssp.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/dssp.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/hbond-insert.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/hbond-insert.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/hbond.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/hbond.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/hpr-wheel.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/hpr-wheel.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/msdwater.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/msdwater.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/ngmxdump.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/ngmxdump.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/phipsi.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/phipsi.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/rama.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rama.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/rdfO-O.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rdfO-O.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2022.5/docs/reference-manual/analysis/plots/rdf.pdf /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rdf.pdf cd /build/reproducible-path/gromacs-2022.5/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2022.5/build/documentation/docs/sphinx-input-rst-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' [ 35%] Built target sphinx-input-rst /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/docs /build/reproducible-path/gromacs-2022.5/build/documentation /build/reproducible-path/gromacs-2022.5/build/documentation/docs /build/reproducible-path/gromacs-2022.5/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' [ 35%] Built target sphinx-input make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' [ 36%] Built target tng_io_obj /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd /build/reproducible-path/gromacs-2022.5/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2022.5 /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2022.5/build/documentation /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs/modularsimulator 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_link_script CMakeFiles/muparser.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libmuparser.so.2 -o ../../lib/libmuparser.so.2.3.4 CMakeFiles/muparser.dir/src/muParser.cpp.o CMakeFiles/muparser.dir/src/muParserBase.cpp.o CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o CMakeFiles/muparser.dir/src/muParserCallback.cpp.o CMakeFiles/muparser.dir/src/muParserDLL.cpp.o CMakeFiles/muparser.dir/src/muParserError.cpp.o CMakeFiles/muparser.dir/src/muParserInt.cpp.o CMakeFiles/muparser.dir/src/muParserTest.cpp.o CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o -Wl,-rpath,"\$ORIGIN/../lib" cd /build/reproducible-path/gromacs-2022.5/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_symlink_library ../../lib/libmuparser.so.2.3.4 ../../lib/libmuparser.so.2 ../../lib/libmuparser.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' [ 38%] Built target muparser make[4]: Leaving directory '/build/reproducible-path/gromacs-2022.5/build/documentation' [ 39%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2022.5/build/documentation' cd 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/baseversion.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/keyvaluetreeserializer.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/keyvaluetreetransform.cpp cd 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/utility/smalloc.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 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-I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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/build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include 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/build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 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-ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/domdec_constraints.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/math/invertmatrix.cpp cd 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CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -MF CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o.d -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/edsam.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pulling/output.cpp.o -MF CMakeFiles/libgromacs.dir/pulling/output.cpp.o.d -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_bundle.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_confrms.cpp /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp: In function 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)': /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp:841:24: warning: '%s' directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 841 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, from /usr/include/c++/12/bits/basic_string.h:3960, from /usr/include/c++/12/string:53, from /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)' at /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp:841:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 4098 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp: In function 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)': /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp:841:24: warning: '%s' directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 841 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)' at /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp:841:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 4098 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp: In function 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)': /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp:841:24: warning: '%s' directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 841 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)' at /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_anaeig.cpp:841:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 4098 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include 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src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_densorder.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_dielectric.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_do_dssp.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_helixorient.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_hydorder.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_lie.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_polystat.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_potential.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem 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-I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/gmx_sham.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/hxprops.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs 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-I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/add_par.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/calch.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/gen_vsite.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/genconf.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/insert_molecules.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/nm2type.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/integrate.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c 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cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/modules/frameaverager.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/modules/histogram.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/modules/lifetime.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/coordinatefile.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadaptercontainer.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/outputselector.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setatoms.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setforces.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setprecision.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/settimestep.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/outputadapters/setvelocities.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/requirements.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/analysismodule.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/analysissettings.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules.cpp cd 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/msd.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/msd.cpp cd 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/rdf.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/sasa.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/modules/select.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/tools/report_methods.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/groupcoord.cpp cd 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src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include 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CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include 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cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/resethandler.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/coordstate.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationhistory.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/histogramsize.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/pointstate.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/read_params.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/awh/read_params.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfitting.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingamplitudelookup.cpp.o -c 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingforceprovider.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingoutputprovider.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/bonded.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/disre.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/listed_forces_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/hostallocator.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/detecthardware.cpp cd 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cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/hardwaretopology.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/printhardware.cpp cd 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/handlerestart.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/logging.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/multisim.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/printtime.cpp cd 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -MF CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o.d -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/options/abstractoption.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/gmxfio_xdr.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/groio.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/libxdrf.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/compiler.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/evaluate.cpp cd 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/build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/scanner_internal.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selection.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectioncollection.cpp /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullCoordEntry]': /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: warning: 'this' pointer is null [-Wnonnull] 828 | vector->resize(numElemInTheFile); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64, from /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.h:40, from /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:39: /usr/include/c++/12/bits/stl_vector.h:1008:7: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]' 1008 | resize(size_type __new_size) | ^~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectionoption.cpp /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = double; AllocatorType = std::allocator; Enum = StatePullGroupEntry]': /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: warning: 'this' pointer is null [-Wnonnull] 828 | vector->resize(numElemInTheFile); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1008:7: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = double; _Alloc = std::allocator]' 1008 | resize(size_type __new_size) | ^~~~~~ /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateFepEntry]': /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: warning: 'this' pointer is null [-Wnonnull] 828 | vector->resize(numElemInTheFile); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1008:7: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = float; _Alloc = std::allocator]' 1008 | resize(size_type __new_size) | ^~~~~~ /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateFepEntry]': /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: warning: 'this' pointer is null [-Wnonnull] 828 | vector->resize(numElemInTheFile); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1008:7: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]' 1008 | resize(size_type __new_size) | ^~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectionoptionbehavior.cpp /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEnergyEntry]': /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: warning: 'this' pointer is null [-Wnonnull] 828 | vector->resize(numElemInTheFile); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1008:7: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]' 1008 | resize(size_type __new_size) | ^~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selectionoptionmanager.cpp /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = std::allocator; Enum = StateKineticEntry]': /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: warning: 'this' pointer is null [-Wnonnull] 828 | vector->resize(numElemInTheFile); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1008:7: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = float; _Alloc = std::allocator]' 1008 | resize(size_type __new_size) | ^~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selelem.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selelem.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include 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-isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selhelp.cpp /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateKineticEntry]': /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: warning: 'this' pointer is null [-Wnonnull] 828 | vector->resize(numElemInTheFile); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1008:7: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]' 1008 | resize(size_type __new_size) | ^~~~~~ /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = int; AllocatorType = std::allocator; Enum = StateEntry]': /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: warning: 'this' pointer is null [-Wnonnull] 828 | vector->resize(numElemInTheFile); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1008:7: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = int; _Alloc = std::allocator]' 1008 | resize(size_type __new_size) | ^~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selmethod.cpp cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2022.5/src/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/src/include -I/build/reproducible-path/gromacs-2022.5/src -I/build/reproducible-path/gromacs-2022.5/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/math/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/options/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/random/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /build/reproducible-path/gromacs-2022.5/src/gromacs/selection/selvalue.cpp /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp: In function 'int doVectorLow(XDR*, Enum, int, int, int*, T**, std::vector<_Tp, _Alloc>*, FILE*, CptElementType) [with T = float; AllocatorType = gmx::Allocator; Enum = StateEntry]': /build/reproducible-path/gromacs-2022.5/src/gromacs/fileio/checkpoint.cpp:828:31: warning: 'this' pointer is null [-Wnonnull] 828 | vector->resize(numElemInTheFile); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1008:7: note: in a call to non-static member function 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = float; _Alloc = gmx::Allocator]' 1008 | resize(size_type __new_size) | ^~~~~~ cd /build/reproducible-path/gromacs-2022.5/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2022.5/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2022.5/src/external -isystem /build/reproducible-path/gromacs-2022.5/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2022.5/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2022.5/src/external/lmfit -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2022.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-unknown-pragmas -Wno-missing-field-initializers -fno-inline -std=c++17 -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c 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